Starting phenix.real_space_refine on Fri Aug 22 22:33:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dph_27635/08_2025/8dph_27635_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dph_27635/08_2025/8dph_27635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dph_27635/08_2025/8dph_27635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dph_27635/08_2025/8dph_27635.map" model { file = "/net/cci-nas-00/data/ceres_data/8dph_27635/08_2025/8dph_27635_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dph_27635/08_2025/8dph_27635_trim.cif" } resolution = 3.2 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 Cl 1 4.86 5 C 5259 2.51 5 N 1367 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8182 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1933 Classifications: {'peptide': 264} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 2, 'ARG:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1683 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 9, 'ASP:plan': 7, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2479 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 4, 'ARG:plan': 9, 'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 284 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1734 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'CLR': 2, 'T4U': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.71, per 1000 atoms: 0.21 Number of scatterers: 8182 At special positions: 0 Unit cell: (89.18, 120.12, 134.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 56 16.00 O 1499 8.00 N 1367 7.00 C 5259 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 0.47 Conformation dependent library (CDL) restraints added in 411.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 38.8% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.501A pdb=" N ILE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 removed outlier: 5.035A pdb=" N PHE A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.555A pdb=" N SER A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 158 removed outlier: 4.237A pdb=" N SER A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 removed outlier: 3.669A pdb=" N HIS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.714A pdb=" N ALA A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.933A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 removed outlier: 6.954A pdb=" N GLU A 198 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 removed outlier: 4.410A pdb=" N ILE A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 245 removed outlier: 3.508A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 337 removed outlier: 4.270A pdb=" N GLU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Proline residue: A 326 - end of helix removed outlier: 3.604A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.753A pdb=" N VAL A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TRP A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.862A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.515A pdb=" N THR B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.515A pdb=" N CYS B 99 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (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 145 through 156 removed outlier: 3.778A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 185 through 203 removed outlier: 3.881A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.682A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 24 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.559A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.642A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.506A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.645A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.543A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N GLY B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.649A 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: 6.771A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.357A 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: 3.709A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.964A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.629A 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: 6.839A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.977A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.337A 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: 6.544A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.045A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.839A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.298A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.787A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1092 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: 1.03 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1315 1.31 - 1.44: 2288 1.44 - 1.56: 4667 1.56 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 8353 Sorted by residual: bond pdb=" C10 T4U A 501 " pdb="CL12 T4U A 501 " ideal model delta sigma weight residual 1.757 1.515 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C09 T4U A 501 " pdb=" C11 T4U A 501 " ideal model delta sigma weight residual 1.408 1.280 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C03 T4U A 501 " pdb=" C10 T4U A 501 " ideal model delta sigma weight residual 1.383 1.276 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C04 T4U A 501 " pdb=" C09 T4U A 501 " ideal model delta sigma weight residual 1.508 1.414 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" N VAL A 156 " pdb=" CA VAL A 156 " ideal model delta sigma weight residual 1.458 1.517 -0.059 1.29e-02 6.01e+03 2.08e+01 ... (remaining 8348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11251 2.00 - 3.99: 114 3.99 - 5.99: 21 5.99 - 7.98: 2 7.98 - 9.98: 3 Bond angle restraints: 11391 Sorted by residual: angle pdb=" O ALA A 155 " pdb=" C ALA A 155 " pdb=" N VAL A 156 " ideal model delta sigma weight residual 122.46 116.74 5.72 1.38e+00 5.25e-01 1.72e+01 angle pdb=" N PRO A 159 " pdb=" CA PRO A 159 " pdb=" C PRO A 159 " ideal model delta sigma weight residual 113.57 118.98 -5.41 1.31e+00 5.83e-01 1.71e+01 angle pdb=" N TRP A 130 " pdb=" CA TRP A 130 " pdb=" C TRP A 130 " ideal model delta sigma weight residual 110.97 106.64 4.33 1.09e+00 8.42e-01 1.58e+01 angle pdb=" CA TRP A 130 " pdb=" CB TRP A 130 " pdb=" CG TRP A 130 " ideal model delta sigma weight residual 113.60 120.77 -7.17 1.90e+00 2.77e-01 1.43e+01 angle pdb=" C SER A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta sigma weight residual 119.19 123.08 -3.89 1.06e+00 8.90e-01 1.35e+01 ... (remaining 11386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 4792 17.27 - 34.54: 146 34.54 - 51.80: 32 51.80 - 69.07: 5 69.07 - 86.34: 3 Dihedral angle restraints: 4978 sinusoidal: 1816 harmonic: 3162 Sorted by residual: dihedral pdb=" CA ALA E 131 " pdb=" C ALA E 131 " pdb=" N THR E 132 " pdb=" CA THR E 132 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA PHE A 223 " pdb=" C PHE A 223 " pdb=" N PHE A 224 " pdb=" CA PHE A 224 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB GLU A 161 " pdb=" CG GLU A 161 " pdb=" CD GLU A 161 " pdb=" OE1 GLU A 161 " ideal model delta sinusoidal sigma weight residual 0.00 86.34 -86.34 1 3.00e+01 1.11e-03 9.99e+00 ... (remaining 4975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1264 0.089 - 0.178: 84 0.178 - 0.267: 4 0.267 - 0.357: 0 0.357 - 0.446: 1 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CB VAL A 156 " pdb=" CA VAL A 156 " pdb=" CG1 VAL A 156 " pdb=" CG2 VAL A 156 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA PRO A 159 " pdb=" N PRO A 159 " pdb=" C PRO A 159 " pdb=" CB PRO A 159 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ARG A 157 " pdb=" N ARG A 157 " pdb=" C ARG A 157 " pdb=" CB ARG A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1350 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 155 " -0.019 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ALA A 155 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA A 155 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 156 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 T4U A 501 " 0.005 2.00e-02 2.50e+03 1.54e-02 5.32e+00 pdb=" C03 T4U A 501 " 0.017 2.00e-02 2.50e+03 pdb=" C04 T4U A 501 " -0.013 2.00e-02 2.50e+03 pdb=" C06 T4U A 501 " 0.009 2.00e-02 2.50e+03 pdb=" C08 T4U A 501 " 0.012 2.00e-02 2.50e+03 pdb=" C09 T4U A 501 " -0.011 2.00e-02 2.50e+03 pdb=" C10 T4U A 501 " 0.019 2.00e-02 2.50e+03 pdb=" C11 T4U A 501 " -0.009 2.00e-02 2.50e+03 pdb="CL12 T4U A 501 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.023 5.00e-02 4.00e+02 3.56e-02 2.02e+00 pdb=" N PRO C 236 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.020 5.00e-02 4.00e+02 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 154 2.71 - 3.26: 7606 3.26 - 3.80: 12043 3.80 - 4.35: 15220 4.35 - 4.90: 26835 Nonbonded interactions: 61858 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.162 3.040 nonbonded pdb=" OD2 ASP A 151 " pdb=" OH TYR B 243 " model vdw 2.207 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.229 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.260 3.040 nonbonded pdb=" NH1 ARG B 93 " pdb=" OD1 ASP B 124 " model vdw 2.268 3.120 ... (remaining 61853 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: 1.090 Set stop_for_unknowns flag: 0.010 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 0.242 8355 Z= 0.245 Angle : 0.558 9.975 11395 Z= 0.311 Chirality : 0.045 0.446 1353 Planarity : 0.003 0.036 1423 Dihedral : 9.344 86.338 2926 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.73 % Allowed : 1.71 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.66 (0.26), residues: 1065 helix: 2.09 (0.30), residues: 328 sheet: 1.31 (0.30), residues: 293 loop : 0.28 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 132 TYR 0.007 0.001 TYR C 105 PHE 0.012 0.001 PHE C 199 TRP 0.019 0.001 TRP A 130 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8353) covalent geometry : angle 0.55777 (11391) SS BOND : bond 0.00293 ( 2) SS BOND : angle 0.91477 ( 4) hydrogen bonds : bond 0.21830 ( 394) hydrogen bonds : angle 6.22533 ( 1092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 261 time to evaluate : 0.188 Fit side-chains REVERT: A 153 TYR cc_start: 0.8228 (t80) cc_final: 0.8000 (t80) REVERT: A 318 PHE cc_start: 0.6966 (m-80) cc_final: 0.6686 (m-80) REVERT: B 136 THR cc_start: 0.8155 (p) cc_final: 0.7913 (t) REVERT: B 216 THR cc_start: 0.7833 (p) cc_final: 0.7551 (p) REVERT: B 219 VAL cc_start: 0.6831 (OUTLIER) cc_final: 0.6607 (p) REVERT: B 230 ASP cc_start: 0.7256 (m-30) cc_final: 0.7053 (m-30) REVERT: C 48 ARG cc_start: 0.7579 (mmt180) cc_final: 0.7270 (mmt-90) REVERT: C 98 SER cc_start: 0.7962 (p) cc_final: 0.7740 (p) REVERT: C 100 VAL cc_start: 0.8604 (p) cc_final: 0.8315 (t) REVERT: C 150 ARG cc_start: 0.8334 (mmt-90) cc_final: 0.8088 (mmt180) REVERT: C 168 LEU cc_start: 0.7997 (tp) cc_final: 0.7757 (tt) REVERT: C 325 MET cc_start: 0.6588 (mtt) cc_final: 0.6323 (mmm) REVERT: C 340 ASN cc_start: 0.7330 (t0) cc_final: 0.6931 (t0) REVERT: E 23 SER cc_start: 0.8307 (m) cc_final: 0.7963 (t) REVERT: E 98 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.7387 (ptt180) REVERT: E 185 SER cc_start: 0.7835 (t) cc_final: 0.7606 (p) REVERT: E 190 ARG cc_start: 0.7835 (mtm110) cc_final: 0.7322 (mtm110) outliers start: 6 outliers final: 4 residues processed: 265 average time/residue: 0.0857 time to fit residues: 30.4460 Evaluate side-chains 213 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TRP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 219 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0470 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN B 244 ASN C 88 ASN C 110 ASN C 119 ASN C 220 GLN C 230 ASN E 35 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.129332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113118 restraints weight = 12830.302| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.03 r_work: 0.3325 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8355 Z= 0.146 Angle : 0.573 7.973 11395 Z= 0.306 Chirality : 0.044 0.228 1353 Planarity : 0.004 0.049 1423 Dihedral : 5.280 46.852 1307 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.93 % Allowed : 9.52 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.74 (0.26), residues: 1065 helix: 2.27 (0.29), residues: 338 sheet: 1.50 (0.31), residues: 278 loop : 0.10 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 137 TYR 0.015 0.001 TYR E 178 PHE 0.018 0.002 PHE C 199 TRP 0.010 0.001 TRP C 332 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8353) covalent geometry : angle 0.57247 (11391) SS BOND : bond 0.00447 ( 2) SS BOND : angle 0.72421 ( 4) hydrogen bonds : bond 0.05311 ( 394) hydrogen bonds : angle 4.41205 ( 1092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.302 Fit side-chains REVERT: A 146 CYS cc_start: 0.7921 (t) cc_final: 0.7616 (m) REVERT: A 153 TYR cc_start: 0.8495 (t80) cc_final: 0.8273 (t80) REVERT: A 325 CYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8126 (m) REVERT: B 126 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7979 (pttp) REVERT: B 136 THR cc_start: 0.8482 (p) cc_final: 0.8196 (t) REVERT: B 194 ARG cc_start: 0.8443 (ttp80) cc_final: 0.8075 (ttp-110) REVERT: C 75 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7367 (mm-40) REVERT: C 98 SER cc_start: 0.8326 (p) cc_final: 0.7849 (t) REVERT: C 150 ARG cc_start: 0.8538 (mmt-90) cc_final: 0.8265 (mmt-90) REVERT: C 258 ASP cc_start: 0.6171 (t0) cc_final: 0.5478 (t0) REVERT: C 303 ASP cc_start: 0.7297 (m-30) cc_final: 0.6964 (p0) REVERT: C 325 MET cc_start: 0.7813 (mtt) cc_final: 0.7420 (mmm) REVERT: E 23 SER cc_start: 0.8412 (m) cc_final: 0.8109 (t) REVERT: E 103 TYR cc_start: 0.8656 (t80) cc_final: 0.8440 (t80) REVERT: E 185 SER cc_start: 0.8135 (t) cc_final: 0.7879 (p) REVERT: E 190 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7775 (mtm110) outliers start: 24 outliers final: 14 residues processed: 230 average time/residue: 0.0868 time to fit residues: 26.6287 Evaluate side-chains 222 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 88 ASN C 110 ASN C 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111964 restraints weight = 12728.199| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.03 r_work: 0.3309 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8355 Z= 0.139 Angle : 0.540 7.732 11395 Z= 0.292 Chirality : 0.043 0.219 1353 Planarity : 0.004 0.056 1423 Dihedral : 4.919 39.981 1304 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.30 % Allowed : 11.23 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.73 (0.26), residues: 1065 helix: 2.42 (0.29), residues: 334 sheet: 1.58 (0.30), residues: 284 loop : -0.11 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 137 TYR 0.012 0.001 TYR E 178 PHE 0.019 0.002 PHE C 241 TRP 0.011 0.002 TRP C 169 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8353) covalent geometry : angle 0.53970 (11391) SS BOND : bond 0.00377 ( 2) SS BOND : angle 0.66036 ( 4) hydrogen bonds : bond 0.05130 ( 394) hydrogen bonds : angle 4.10513 ( 1092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.219 Fit side-chains REVERT: A 146 CYS cc_start: 0.7990 (t) cc_final: 0.7701 (m) REVERT: A 153 TYR cc_start: 0.8490 (t80) cc_final: 0.8279 (t80) REVERT: A 325 CYS cc_start: 0.8318 (m) cc_final: 0.8099 (m) REVERT: B 35 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7817 (mtm180) REVERT: B 126 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7967 (pttp) REVERT: B 136 THR cc_start: 0.8584 (p) cc_final: 0.8249 (t) REVERT: B 194 ARG cc_start: 0.8380 (ttp80) cc_final: 0.8125 (ttp-110) REVERT: C 48 ARG cc_start: 0.8073 (mmt180) cc_final: 0.7778 (mmt-90) REVERT: C 98 SER cc_start: 0.8354 (p) cc_final: 0.7939 (t) REVERT: C 100 VAL cc_start: 0.8675 (p) cc_final: 0.8451 (t) REVERT: C 258 ASP cc_start: 0.6272 (t0) cc_final: 0.5570 (t0) REVERT: C 303 ASP cc_start: 0.7402 (m-30) cc_final: 0.7169 (p0) REVERT: C 325 MET cc_start: 0.7802 (mtt) cc_final: 0.7573 (mmm) REVERT: E 23 SER cc_start: 0.8418 (m) cc_final: 0.8090 (t) REVERT: E 93 MET cc_start: 0.7991 (tpp) cc_final: 0.7322 (ttm) REVERT: E 190 ARG cc_start: 0.8041 (mtm110) cc_final: 0.7692 (mtm110) outliers start: 27 outliers final: 20 residues processed: 224 average time/residue: 0.0844 time to fit residues: 24.9825 Evaluate side-chains 224 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 51 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN C 88 ASN C 110 ASN C 119 ASN C 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110137 restraints weight = 13029.625| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.00 r_work: 0.3280 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8355 Z= 0.173 Angle : 0.578 7.074 11395 Z= 0.313 Chirality : 0.045 0.220 1353 Planarity : 0.004 0.067 1423 Dihedral : 5.005 38.009 1302 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.91 % Allowed : 11.84 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.57 (0.26), residues: 1065 helix: 2.29 (0.29), residues: 336 sheet: 1.55 (0.30), residues: 282 loop : -0.26 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 137 TYR 0.012 0.002 TYR C 105 PHE 0.019 0.002 PHE A 328 TRP 0.012 0.002 TRP B 96 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8353) covalent geometry : angle 0.57817 (11391) SS BOND : bond 0.00416 ( 2) SS BOND : angle 0.68463 ( 4) hydrogen bonds : bond 0.05671 ( 394) hydrogen bonds : angle 4.15586 ( 1092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.293 Fit side-chains REVERT: A 63 ILE cc_start: 0.6344 (pt) cc_final: 0.6089 (mm) REVERT: A 146 CYS cc_start: 0.8101 (t) cc_final: 0.7585 (m) REVERT: A 153 TYR cc_start: 0.8552 (t80) cc_final: 0.8306 (t80) REVERT: A 325 CYS cc_start: 0.8332 (m) cc_final: 0.8098 (m) REVERT: B 136 THR cc_start: 0.8575 (p) cc_final: 0.8128 (t) REVERT: B 194 ARG cc_start: 0.8337 (ttp80) cc_final: 0.8089 (ttp-110) REVERT: C 61 MET cc_start: 0.8091 (ppp) cc_final: 0.7612 (ppp) REVERT: C 79 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8109 (mt) REVERT: C 98 SER cc_start: 0.8393 (p) cc_final: 0.8061 (t) REVERT: C 100 VAL cc_start: 0.8690 (p) cc_final: 0.8432 (t) REVERT: C 143 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8116 (m) REVERT: C 227 SER cc_start: 0.8331 (m) cc_final: 0.8105 (t) REVERT: C 258 ASP cc_start: 0.6353 (t0) cc_final: 0.5670 (t0) REVERT: C 325 MET cc_start: 0.7757 (mtt) cc_final: 0.7371 (mmm) REVERT: E 23 SER cc_start: 0.8429 (m) cc_final: 0.8088 (t) REVERT: E 88 SER cc_start: 0.7383 (OUTLIER) cc_final: 0.7158 (t) outliers start: 32 outliers final: 21 residues processed: 222 average time/residue: 0.0815 time to fit residues: 24.1894 Evaluate side-chains 230 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN C 110 ASN C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110710 restraints weight = 12903.145| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.97 r_work: 0.3291 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8355 Z= 0.152 Angle : 0.556 6.952 11395 Z= 0.299 Chirality : 0.044 0.219 1353 Planarity : 0.004 0.062 1423 Dihedral : 4.913 38.235 1302 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.42 % Allowed : 12.94 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.52 (0.26), residues: 1065 helix: 2.27 (0.28), residues: 341 sheet: 1.55 (0.31), residues: 282 loop : -0.37 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.013 0.001 TYR E 59 PHE 0.013 0.002 PHE C 241 TRP 0.010 0.002 TRP B 96 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8353) covalent geometry : angle 0.55573 (11391) SS BOND : bond 0.00395 ( 2) SS BOND : angle 0.74416 ( 4) hydrogen bonds : bond 0.05207 ( 394) hydrogen bonds : angle 4.03266 ( 1092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.240 Fit side-chains REVERT: A 63 ILE cc_start: 0.6312 (pt) cc_final: 0.6054 (mm) REVERT: A 146 CYS cc_start: 0.8069 (t) cc_final: 0.7615 (m) REVERT: A 325 CYS cc_start: 0.8287 (m) cc_final: 0.8053 (m) REVERT: B 194 ARG cc_start: 0.8296 (ttp80) cc_final: 0.8046 (ttp-110) REVERT: C 48 ARG cc_start: 0.8049 (mmt180) cc_final: 0.7828 (mmt-90) REVERT: C 61 MET cc_start: 0.8134 (ppp) cc_final: 0.7560 (ppp) REVERT: C 79 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8098 (mt) REVERT: C 98 SER cc_start: 0.8399 (p) cc_final: 0.8095 (t) REVERT: C 100 VAL cc_start: 0.8689 (p) cc_final: 0.8443 (t) REVERT: C 227 SER cc_start: 0.8258 (m) cc_final: 0.8040 (t) REVERT: C 258 ASP cc_start: 0.6402 (t0) cc_final: 0.5753 (t0) REVERT: C 325 MET cc_start: 0.7626 (mtt) cc_final: 0.7329 (mmm) REVERT: C 340 ASN cc_start: 0.7776 (t0) cc_final: 0.7563 (t0) REVERT: E 23 SER cc_start: 0.8404 (m) cc_final: 0.8060 (t) REVERT: E 88 SER cc_start: 0.7331 (OUTLIER) cc_final: 0.7101 (t) REVERT: E 93 MET cc_start: 0.8064 (tpp) cc_final: 0.7350 (tpp) outliers start: 28 outliers final: 22 residues processed: 223 average time/residue: 0.0886 time to fit residues: 26.3081 Evaluate side-chains 231 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 88 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 77 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.111931 restraints weight = 12838.740| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.97 r_work: 0.3308 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8355 Z= 0.124 Angle : 0.524 6.826 11395 Z= 0.280 Chirality : 0.043 0.219 1353 Planarity : 0.004 0.055 1423 Dihedral : 4.747 38.221 1302 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.93 % Allowed : 15.02 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.60 (0.26), residues: 1065 helix: 2.36 (0.28), residues: 341 sheet: 1.55 (0.30), residues: 281 loop : -0.31 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.012 0.001 TYR E 178 PHE 0.015 0.001 PHE A 137 TRP 0.010 0.001 TRP B 96 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8353) covalent geometry : angle 0.52371 (11391) SS BOND : bond 0.00343 ( 2) SS BOND : angle 0.61284 ( 4) hydrogen bonds : bond 0.04620 ( 394) hydrogen bonds : angle 3.89006 ( 1092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.315 Fit side-chains REVERT: A 63 ILE cc_start: 0.6311 (pt) cc_final: 0.6057 (mm) REVERT: A 146 CYS cc_start: 0.7990 (t) cc_final: 0.7587 (m) REVERT: A 165 PHE cc_start: 0.6759 (t80) cc_final: 0.6547 (t80) REVERT: A 318 PHE cc_start: 0.7314 (m-80) cc_final: 0.7101 (m-80) REVERT: A 325 CYS cc_start: 0.8346 (m) cc_final: 0.8072 (m) REVERT: A 346 MET cc_start: 0.5231 (mmm) cc_final: 0.4995 (mmp) REVERT: C 48 ARG cc_start: 0.8049 (mmt180) cc_final: 0.7827 (mmt-90) REVERT: C 61 MET cc_start: 0.8177 (ppp) cc_final: 0.7652 (ppp) REVERT: C 79 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8063 (mt) REVERT: C 98 SER cc_start: 0.8440 (p) cc_final: 0.8139 (t) REVERT: C 100 VAL cc_start: 0.8671 (p) cc_final: 0.8429 (t) REVERT: C 227 SER cc_start: 0.8224 (m) cc_final: 0.8014 (t) REVERT: C 258 ASP cc_start: 0.6411 (t0) cc_final: 0.5776 (t0) REVERT: C 325 MET cc_start: 0.7565 (mtt) cc_final: 0.7220 (mmm) REVERT: C 340 ASN cc_start: 0.7787 (t0) cc_final: 0.7576 (t0) REVERT: E 23 SER cc_start: 0.8331 (m) cc_final: 0.8005 (t) REVERT: E 93 MET cc_start: 0.8061 (tpp) cc_final: 0.7562 (ttm) outliers start: 24 outliers final: 21 residues processed: 217 average time/residue: 0.1032 time to fit residues: 29.8207 Evaluate side-chains 230 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 101 optimal weight: 0.0060 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 0.0470 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN C 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113310 restraints weight = 13027.042| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.99 r_work: 0.3330 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8355 Z= 0.101 Angle : 0.491 6.720 11395 Z= 0.262 Chirality : 0.043 0.219 1353 Planarity : 0.003 0.048 1423 Dihedral : 4.582 37.797 1302 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.32 % Allowed : 15.75 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.73 (0.26), residues: 1065 helix: 2.51 (0.28), residues: 342 sheet: 1.63 (0.31), residues: 281 loop : -0.28 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 179 TYR 0.012 0.001 TYR E 178 PHE 0.012 0.001 PHE A 328 TRP 0.012 0.001 TRP B 96 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8353) covalent geometry : angle 0.49062 (11391) SS BOND : bond 0.00308 ( 2) SS BOND : angle 1.00449 ( 4) hydrogen bonds : bond 0.03920 ( 394) hydrogen bonds : angle 3.76472 ( 1092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.314 Fit side-chains REVERT: A 63 ILE cc_start: 0.6288 (pt) cc_final: 0.6029 (mm) REVERT: B 48 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7421 (p) REVERT: C 48 ARG cc_start: 0.8053 (mmt180) cc_final: 0.7846 (mmt-90) REVERT: C 61 MET cc_start: 0.8187 (ppp) cc_final: 0.7557 (ppp) REVERT: C 79 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8023 (mt) REVERT: C 98 SER cc_start: 0.8435 (p) cc_final: 0.8146 (t) REVERT: C 100 VAL cc_start: 0.8647 (p) cc_final: 0.8400 (t) REVERT: C 258 ASP cc_start: 0.6401 (t0) cc_final: 0.5778 (t0) REVERT: C 325 MET cc_start: 0.7556 (mtt) cc_final: 0.7196 (mmm) REVERT: C 340 ASN cc_start: 0.7782 (t0) cc_final: 0.7546 (t0) REVERT: E 23 SER cc_start: 0.8290 (m) cc_final: 0.7959 (t) REVERT: E 93 MET cc_start: 0.8057 (tpp) cc_final: 0.7570 (ttm) outliers start: 19 outliers final: 15 residues processed: 215 average time/residue: 0.1055 time to fit residues: 30.0682 Evaluate side-chains 221 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 110 ASN C 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.110667 restraints weight = 12890.299| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.97 r_work: 0.3288 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8355 Z= 0.162 Angle : 0.568 7.022 11395 Z= 0.303 Chirality : 0.044 0.218 1353 Planarity : 0.004 0.066 1423 Dihedral : 4.875 38.160 1302 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.30 % Allowed : 15.02 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.53 (0.26), residues: 1065 helix: 2.39 (0.28), residues: 343 sheet: 1.53 (0.31), residues: 278 loop : -0.45 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 194 TYR 0.012 0.002 TYR E 59 PHE 0.014 0.002 PHE C 151 TRP 0.014 0.002 TRP B 96 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8353) covalent geometry : angle 0.56723 (11391) SS BOND : bond 0.00489 ( 2) SS BOND : angle 1.21600 ( 4) hydrogen bonds : bond 0.05268 ( 394) hydrogen bonds : angle 3.95940 ( 1092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.364 Fit side-chains REVERT: A 63 ILE cc_start: 0.6314 (pt) cc_final: 0.6098 (mm) REVERT: A 146 CYS cc_start: 0.8018 (t) cc_final: 0.7655 (m) REVERT: A 165 PHE cc_start: 0.6789 (t80) cc_final: 0.6494 (t80) REVERT: A 318 PHE cc_start: 0.7282 (m-80) cc_final: 0.7078 (m-80) REVERT: A 325 CYS cc_start: 0.8396 (m) cc_final: 0.8156 (m) REVERT: B 48 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.7494 (p) REVERT: C 48 ARG cc_start: 0.8015 (mmt180) cc_final: 0.7808 (mmt-90) REVERT: C 61 MET cc_start: 0.8140 (ppp) cc_final: 0.7575 (ppp) REVERT: C 79 LEU cc_start: 0.8338 (mp) cc_final: 0.8092 (mt) REVERT: C 98 SER cc_start: 0.8452 (p) cc_final: 0.8197 (t) REVERT: C 100 VAL cc_start: 0.8678 (p) cc_final: 0.8418 (t) REVERT: C 258 ASP cc_start: 0.6481 (t0) cc_final: 0.5889 (t0) REVERT: C 340 ASN cc_start: 0.7779 (t0) cc_final: 0.7549 (t0) REVERT: E 23 SER cc_start: 0.8363 (m) cc_final: 0.8025 (t) REVERT: E 88 SER cc_start: 0.7263 (OUTLIER) cc_final: 0.7023 (t) REVERT: E 93 MET cc_start: 0.8078 (tpp) cc_final: 0.7582 (ttm) outliers start: 27 outliers final: 23 residues processed: 220 average time/residue: 0.1044 time to fit residues: 30.4085 Evaluate side-chains 231 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 52 optimal weight: 0.0040 chunk 3 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112339 restraints weight = 12816.223| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.02 r_work: 0.3313 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8355 Z= 0.115 Angle : 0.522 7.130 11395 Z= 0.276 Chirality : 0.043 0.218 1353 Planarity : 0.004 0.050 1423 Dihedral : 4.639 38.291 1302 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.44 % Allowed : 15.63 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.65 (0.26), residues: 1065 helix: 2.55 (0.28), residues: 343 sheet: 1.53 (0.31), residues: 283 loop : -0.40 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 194 TYR 0.013 0.001 TYR E 178 PHE 0.011 0.001 PHE C 199 TRP 0.014 0.001 TRP B 96 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8353) covalent geometry : angle 0.52161 (11391) SS BOND : bond 0.00320 ( 2) SS BOND : angle 0.83496 ( 4) hydrogen bonds : bond 0.04285 ( 394) hydrogen bonds : angle 3.78852 ( 1092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.283 Fit side-chains REVERT: A 63 ILE cc_start: 0.6290 (pt) cc_final: 0.6049 (mm) REVERT: A 346 MET cc_start: 0.5142 (mmm) cc_final: 0.4901 (mmp) REVERT: B 48 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7461 (p) REVERT: C 61 MET cc_start: 0.8141 (ppp) cc_final: 0.7535 (ppp) REVERT: C 79 LEU cc_start: 0.8282 (mp) cc_final: 0.8044 (mt) REVERT: C 98 SER cc_start: 0.8454 (p) cc_final: 0.8205 (t) REVERT: C 100 VAL cc_start: 0.8661 (p) cc_final: 0.8398 (t) REVERT: C 258 ASP cc_start: 0.6473 (t0) cc_final: 0.5874 (t0) REVERT: C 340 ASN cc_start: 0.7810 (t0) cc_final: 0.7558 (t0) REVERT: E 23 SER cc_start: 0.8304 (m) cc_final: 0.7975 (t) REVERT: E 93 MET cc_start: 0.8088 (tpp) cc_final: 0.7620 (ttm) REVERT: E 127 VAL cc_start: 0.8578 (t) cc_final: 0.8309 (m) REVERT: E 194 SER cc_start: 0.8718 (p) cc_final: 0.8484 (p) outliers start: 20 outliers final: 19 residues processed: 212 average time/residue: 0.0960 time to fit residues: 27.1152 Evaluate side-chains 225 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 0.0370 chunk 97 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN C 75 GLN C 110 ASN C 119 ASN C 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111190 restraints weight = 12673.940| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.04 r_work: 0.3294 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8355 Z= 0.138 Angle : 0.550 7.411 11395 Z= 0.290 Chirality : 0.044 0.218 1353 Planarity : 0.004 0.058 1423 Dihedral : 4.736 38.165 1302 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.69 % Allowed : 15.87 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.57 (0.26), residues: 1065 helix: 2.52 (0.28), residues: 344 sheet: 1.54 (0.31), residues: 278 loop : -0.52 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 194 TYR 0.012 0.001 TYR E 178 PHE 0.011 0.001 PHE C 151 TRP 0.014 0.001 TRP B 96 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8353) covalent geometry : angle 0.54973 (11391) SS BOND : bond 0.00370 ( 2) SS BOND : angle 0.88299 ( 4) hydrogen bonds : bond 0.04766 ( 394) hydrogen bonds : angle 3.85435 ( 1092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 0.307 Fit side-chains REVERT: A 63 ILE cc_start: 0.6347 (pt) cc_final: 0.6144 (mm) REVERT: A 146 CYS cc_start: 0.8010 (t) cc_final: 0.7643 (m) REVERT: A 165 PHE cc_start: 0.6801 (t80) cc_final: 0.6511 (t80) REVERT: A 173 MET cc_start: 0.8065 (tmm) cc_final: 0.7736 (tmm) REVERT: B 48 THR cc_start: 0.7786 (OUTLIER) cc_final: 0.7501 (p) REVERT: C 61 MET cc_start: 0.8140 (ppp) cc_final: 0.7575 (ppp) REVERT: C 79 LEU cc_start: 0.8316 (mp) cc_final: 0.8078 (mt) REVERT: C 98 SER cc_start: 0.8459 (p) cc_final: 0.8220 (t) REVERT: C 100 VAL cc_start: 0.8661 (p) cc_final: 0.8403 (t) REVERT: C 258 ASP cc_start: 0.6525 (t0) cc_final: 0.5962 (t0) REVERT: C 340 ASN cc_start: 0.7800 (t0) cc_final: 0.7544 (t0) REVERT: E 23 SER cc_start: 0.8337 (m) cc_final: 0.8001 (t) REVERT: E 88 SER cc_start: 0.7275 (OUTLIER) cc_final: 0.7024 (t) REVERT: E 93 MET cc_start: 0.8116 (tpp) cc_final: 0.7656 (ttm) REVERT: E 127 VAL cc_start: 0.8575 (t) cc_final: 0.8306 (m) REVERT: E 194 SER cc_start: 0.8715 (p) cc_final: 0.8488 (p) outliers start: 22 outliers final: 19 residues processed: 219 average time/residue: 0.0873 time to fit residues: 25.6457 Evaluate side-chains 227 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN C 110 ASN C 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110783 restraints weight = 12866.371| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.98 r_work: 0.3289 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8355 Z= 0.149 Angle : 0.561 7.405 11395 Z= 0.297 Chirality : 0.044 0.218 1353 Planarity : 0.004 0.059 1423 Dihedral : 4.822 38.630 1302 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.69 % Allowed : 16.12 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.50 (0.26), residues: 1065 helix: 2.48 (0.28), residues: 344 sheet: 1.46 (0.31), residues: 278 loop : -0.53 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 194 TYR 0.011 0.001 TYR E 59 PHE 0.011 0.001 PHE C 151 TRP 0.014 0.002 TRP B 96 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8353) covalent geometry : angle 0.56074 (11391) SS BOND : bond 0.00411 ( 2) SS BOND : angle 0.94549 ( 4) hydrogen bonds : bond 0.05077 ( 394) hydrogen bonds : angle 3.91292 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2238.02 seconds wall clock time: 38 minutes 52.41 seconds (2332.41 seconds total)