Starting phenix.real_space_refine on Sat Jul 26 08:39:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xau_33099/07_2025/7xau_33099.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xau_33099/07_2025/7xau_33099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xau_33099/07_2025/7xau_33099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xau_33099/07_2025/7xau_33099.map" model { file = "/net/cci-nas-00/data/ceres_data/7xau_33099/07_2025/7xau_33099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xau_33099/07_2025/7xau_33099.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5351 2.51 5 N 1437 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8443 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1923 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 12, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 178 Chain: "B" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1598 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 119 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Classifications: {'peptide': 3} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 2} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Time building chain proxies: 5.35, per 1000 atoms: 0.63 Number of scatterers: 8443 At special positions: 0 Unit cell: (87.74, 123.05, 123.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1601 8.00 N 1437 7.00 C 5351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.05 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.03 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 Links applied TRANS " DTR F 4 " - " PHE F 3 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN F 1 " pdb=" CB DTR F 4 " Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 32.1% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.648A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.880A pdb=" N ILE A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.820A pdb=" N ILE A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 removed outlier: 3.874A pdb=" N LEU A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.824A pdb=" N MET A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.548A pdb=" N THR A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TRP A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 168 " --> pdb=" O MET A 164 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.969A pdb=" N TYR A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 removed outlier: 4.036A pdb=" N ILE A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.582A pdb=" N ILE A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 removed outlier: 4.131A pdb=" N ILE A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.620A pdb=" N VAL A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.625A pdb=" N SER A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 261 " --> pdb=" O MET A 257 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.606A pdb=" N ASN A 276 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 277 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 removed outlier: 3.841A pdb=" N ASP A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 314 Proline residue: A 309 - end of helix removed outlier: 3.514A pdb=" N TYR A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 326 removed outlier: 3.710A pdb=" N LYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 24 removed outlier: 3.615A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.637A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.651A pdb=" N SER B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.910A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 removed outlier: 3.906A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 removed outlier: 5.173A pdb=" N CYS B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 351 removed outlier: 4.133A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.525A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA C 21 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 7 through 24 removed outlier: 3.768A pdb=" N GLN D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.558A pdb=" N TYR D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 191 through 193 No H-bonds generated for 'chain 'E' and resid 191 through 193' Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 184 removed outlier: 4.129A pdb=" N ARG A 184 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 188 removed outlier: 6.138A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 52 removed outlier: 5.622A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 338 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 4.048A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.025A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.650A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 191 through 192 Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.493A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.645A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.514A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 51 removed outlier: 6.507A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.704A pdb=" N CYS E 159 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE E 212 " --> pdb=" O CYS E 159 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.431A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 243 " --> pdb=" O TYR E 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'E' and resid 189 through 190 286 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2336 1.33 - 1.46: 2330 1.46 - 1.59: 3865 1.59 - 1.71: 0 1.71 - 1.84: 74 Bond restraints: 8605 Sorted by residual: bond pdb=" CA GLU C 138 " pdb=" CB GLU C 138 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.34e-02 5.57e+03 2.48e+01 bond pdb=" C LEU A 270 " pdb=" N PRO A 271 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" CG LEU C 95 " pdb=" CD1 LEU C 95 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.94e+00 bond pdb=" C THR C 243 " pdb=" N GLY C 244 " ideal model delta sigma weight residual 1.332 1.319 0.013 5.00e-03 4.00e+04 6.57e+00 bond pdb=" C CYS C 148 " pdb=" N CYS C 149 " ideal model delta sigma weight residual 1.330 1.365 -0.035 1.39e-02 5.18e+03 6.41e+00 ... (remaining 8600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 11296 2.66 - 5.32: 361 5.32 - 7.98: 50 7.98 - 10.64: 6 10.64 - 13.29: 4 Bond angle restraints: 11717 Sorted by residual: angle pdb=" N LYS A 73 " pdb=" CA LYS A 73 " pdb=" C LYS A 73 " ideal model delta sigma weight residual 111.71 104.67 7.04 1.34e+00 5.57e-01 2.76e+01 angle pdb=" N MET B 243 " pdb=" CA MET B 243 " pdb=" C MET B 243 " ideal model delta sigma weight residual 113.41 107.18 6.23 1.22e+00 6.72e-01 2.60e+01 angle pdb=" N ALA A 72 " pdb=" CA ALA A 72 " pdb=" C ALA A 72 " ideal model delta sigma weight residual 110.53 116.64 -6.11 1.29e+00 6.01e-01 2.24e+01 angle pdb=" N VAL B 201 " pdb=" CA VAL B 201 " pdb=" C VAL B 201 " ideal model delta sigma weight residual 106.21 111.16 -4.95 1.07e+00 8.73e-01 2.14e+01 angle pdb=" C GLN A 187 " pdb=" N TRP A 188 " pdb=" CA TRP A 188 " ideal model delta sigma weight residual 122.46 128.81 -6.35 1.41e+00 5.03e-01 2.03e+01 ... (remaining 11712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4563 17.69 - 35.38: 428 35.38 - 53.07: 68 53.07 - 70.76: 10 70.76 - 88.45: 4 Dihedral angle restraints: 5073 sinusoidal: 1769 harmonic: 3304 Sorted by residual: dihedral pdb=" CA LEU A 105 " pdb=" C LEU A 105 " pdb=" N VAL A 106 " pdb=" CA VAL A 106 " ideal model delta harmonic sigma weight residual 180.00 -134.41 -45.59 0 5.00e+00 4.00e-02 8.31e+01 dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.62 -66.62 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CA TYR A 71 " pdb=" C TYR A 71 " pdb=" N ALA A 72 " pdb=" CA ALA A 72 " ideal model delta harmonic sigma weight residual -180.00 -145.55 -34.45 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 5070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 957 0.057 - 0.113: 322 0.113 - 0.169: 80 0.169 - 0.226: 19 0.226 - 0.282: 8 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CB VAL B 218 " pdb=" CA VAL B 218 " pdb=" CG1 VAL B 218 " pdb=" CG2 VAL B 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE C 270 " pdb=" CA ILE C 270 " pdb=" CG1 ILE C 270 " pdb=" CG2 ILE C 270 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL B 339 " pdb=" CA VAL B 339 " pdb=" CG1 VAL B 339 " pdb=" CG2 VAL B 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1383 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 175 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO A 176 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO C 236 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 308 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO A 309 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.037 5.00e-02 4.00e+02 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 981 2.73 - 3.27: 7741 3.27 - 3.81: 14228 3.81 - 4.36: 17133 4.36 - 4.90: 29082 Nonbonded interactions: 69165 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.187 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.215 3.040 nonbonded pdb=" O THR B 260 " pdb=" OG1 THR B 316 " model vdw 2.252 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.277 3.040 ... (remaining 69160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.620 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 : 0.011 0.087 8610 Z= 0.478 Angle : 1.189 13.295 11728 Z= 0.695 Chirality : 0.063 0.282 1386 Planarity : 0.007 0.073 1490 Dihedral : 14.129 88.451 2924 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.17 % Allowed : 10.04 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.19), residues: 1121 helix: -4.59 (0.13), residues: 322 sheet: -1.96 (0.28), residues: 272 loop : -2.65 (0.22), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP C 99 HIS 0.008 0.002 HIS E 167 PHE 0.037 0.004 PHE C 234 TYR 0.033 0.003 TYR C 59 ARG 0.009 0.001 ARG A 154 Details of bonding type rmsd link_TRANS : bond 0.00397 ( 1) link_TRANS : angle 0.35169 ( 3) hydrogen bonds : bond 0.30934 ( 286) hydrogen bonds : angle 11.55558 ( 792) SS BOND : bond 0.01320 ( 4) SS BOND : angle 2.35036 ( 8) covalent geometry : bond 0.01061 ( 8605) covalent geometry : angle 1.18831 (11717) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7460 (m-80) cc_final: 0.7131 (m-80) REVERT: A 75 LYS cc_start: 0.6087 (mmtm) cc_final: 0.5728 (tptt) REVERT: C 327 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7750 (m) REVERT: E 6 GLU cc_start: 0.7745 (pm20) cc_final: 0.7446 (pm20) outliers start: 10 outliers final: 4 residues processed: 204 average time/residue: 0.9638 time to fit residues: 211.8126 Evaluate side-chains 148 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 102 GLN B 188 HIS B 346 ASN C 6 GLN C 62 HIS ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.198816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.141666 restraints weight = 10640.448| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.76 r_work: 0.3622 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8610 Z= 0.142 Angle : 0.682 11.544 11728 Z= 0.363 Chirality : 0.044 0.197 1386 Planarity : 0.005 0.048 1490 Dihedral : 6.686 45.134 1224 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.92 % Allowed : 18.09 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.21), residues: 1121 helix: -3.42 (0.20), residues: 320 sheet: -1.50 (0.29), residues: 274 loop : -2.30 (0.24), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 62 PHE 0.016 0.002 PHE C 241 TYR 0.025 0.002 TYR A 273 ARG 0.009 0.001 ARG A 155 Details of bonding type rmsd link_TRANS : bond 0.00069 ( 1) link_TRANS : angle 0.13116 ( 3) hydrogen bonds : bond 0.04889 ( 286) hydrogen bonds : angle 6.66270 ( 792) SS BOND : bond 0.00504 ( 4) SS BOND : angle 0.79244 ( 8) covalent geometry : bond 0.00311 ( 8605) covalent geometry : angle 0.68244 (11717) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8153 (mp) cc_final: 0.7835 (tt) REVERT: A 163 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.7980 (m) REVERT: C 241 PHE cc_start: 0.7022 (p90) cc_final: 0.6699 (p90) REVERT: C 243 THR cc_start: 0.8257 (p) cc_final: 0.7922 (p) REVERT: E 6 GLU cc_start: 0.7690 (pm20) cc_final: 0.7157 (pm20) REVERT: E 19 LYS cc_start: 0.8264 (tttp) cc_final: 0.8038 (ptmm) REVERT: E 20 LEU cc_start: 0.8347 (mp) cc_final: 0.8122 (mt) outliers start: 25 outliers final: 10 residues processed: 187 average time/residue: 0.9187 time to fit residues: 185.5872 Evaluate side-chains 150 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.195667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137550 restraints weight = 10781.578| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.77 r_work: 0.3584 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 8610 Z= 0.216 Angle : 0.687 10.556 11728 Z= 0.363 Chirality : 0.045 0.166 1386 Planarity : 0.004 0.044 1490 Dihedral : 6.150 40.239 1221 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.60 % Allowed : 19.25 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.22), residues: 1121 helix: -2.69 (0.23), residues: 320 sheet: -1.27 (0.29), residues: 272 loop : -2.09 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 36 HIS 0.003 0.001 HIS C 311 PHE 0.015 0.002 PHE C 199 TYR 0.015 0.002 TYR E 103 ARG 0.004 0.000 ARG E 18 Details of bonding type rmsd link_TRANS : bond 0.00119 ( 1) link_TRANS : angle 0.13856 ( 3) hydrogen bonds : bond 0.04282 ( 286) hydrogen bonds : angle 6.12597 ( 792) SS BOND : bond 0.00604 ( 4) SS BOND : angle 0.90385 ( 8) covalent geometry : bond 0.00513 ( 8605) covalent geometry : angle 0.68696 (11717) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8261 (m110) REVERT: C 59 TYR cc_start: 0.7816 (m-80) cc_final: 0.7505 (m-80) REVERT: C 241 PHE cc_start: 0.7148 (p90) cc_final: 0.6846 (p90) REVERT: C 252 LEU cc_start: 0.8637 (tt) cc_final: 0.8408 (tp) REVERT: E 6 GLU cc_start: 0.7612 (pm20) cc_final: 0.7151 (pm20) REVERT: E 19 LYS cc_start: 0.8289 (tttp) cc_final: 0.8026 (ptmm) REVERT: E 20 LEU cc_start: 0.8358 (mp) cc_final: 0.8148 (mt) outliers start: 48 outliers final: 26 residues processed: 189 average time/residue: 0.8571 time to fit residues: 175.8857 Evaluate side-chains 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 153 TRP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 55 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.201633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.145816 restraints weight = 10636.115| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.67 r_work: 0.3657 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8610 Z= 0.114 Angle : 0.611 10.918 11728 Z= 0.317 Chirality : 0.042 0.168 1386 Planarity : 0.004 0.036 1490 Dihedral : 5.567 38.289 1221 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.90 % Allowed : 20.89 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.23), residues: 1121 helix: -2.06 (0.25), residues: 319 sheet: -1.19 (0.29), residues: 272 loop : -1.89 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE E 239 TYR 0.012 0.001 TYR A 50 ARG 0.006 0.000 ARG E 18 Details of bonding type rmsd link_TRANS : bond 0.00075 ( 1) link_TRANS : angle 0.17376 ( 3) hydrogen bonds : bond 0.03330 ( 286) hydrogen bonds : angle 5.52945 ( 792) SS BOND : bond 0.00383 ( 4) SS BOND : angle 0.48153 ( 8) covalent geometry : bond 0.00257 ( 8605) covalent geometry : angle 0.61090 (11717) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7885 (m) REVERT: A 273 TYR cc_start: 0.7447 (m-80) cc_final: 0.7119 (m-80) REVERT: B 21 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8303 (ttp80) REVERT: B 326 SER cc_start: 0.8960 (m) cc_final: 0.8653 (p) REVERT: C 44 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6504 (tp-100) REVERT: C 59 TYR cc_start: 0.7606 (m-80) cc_final: 0.7281 (m-80) REVERT: C 61 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7710 (ppp) REVERT: C 241 PHE cc_start: 0.6876 (p90) cc_final: 0.6600 (p90) REVERT: C 243 THR cc_start: 0.8150 (p) cc_final: 0.7873 (p) REVERT: C 290 ASP cc_start: 0.5679 (p0) cc_final: 0.5405 (p0) REVERT: E 6 GLU cc_start: 0.7506 (pm20) cc_final: 0.7069 (pm20) REVERT: E 19 LYS cc_start: 0.8313 (tttp) cc_final: 0.8070 (ptmm) REVERT: E 153 GLU cc_start: 0.5173 (OUTLIER) cc_final: 0.3202 (pp20) REVERT: E 192 MET cc_start: 0.6400 (ttp) cc_final: 0.5133 (tpp) outliers start: 42 outliers final: 22 residues processed: 192 average time/residue: 0.8760 time to fit residues: 182.6540 Evaluate side-chains 173 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.200626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.146121 restraints weight = 10563.940| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.96 r_work: 0.3635 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8610 Z= 0.140 Angle : 0.630 12.699 11728 Z= 0.326 Chirality : 0.043 0.154 1386 Planarity : 0.003 0.034 1490 Dihedral : 5.444 37.877 1221 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.37 % Allowed : 22.05 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.23), residues: 1121 helix: -1.79 (0.26), residues: 323 sheet: -1.04 (0.29), residues: 272 loop : -1.77 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 334 TYR 0.010 0.001 TYR E 103 ARG 0.006 0.000 ARG E 18 Details of bonding type rmsd link_TRANS : bond 0.00096 ( 1) link_TRANS : angle 0.09549 ( 3) hydrogen bonds : bond 0.03270 ( 286) hydrogen bonds : angle 5.41991 ( 792) SS BOND : bond 0.00338 ( 4) SS BOND : angle 0.86539 ( 8) covalent geometry : bond 0.00327 ( 8605) covalent geometry : angle 0.62969 (11717) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7363 (tm) REVERT: A 163 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7921 (m) REVERT: B 14 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: B 21 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8318 (ttp80) REVERT: B 297 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7770 (mp0) REVERT: B 326 SER cc_start: 0.8932 (m) cc_final: 0.8646 (p) REVERT: C 44 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6426 (tp-100) REVERT: C 59 TYR cc_start: 0.7592 (m-80) cc_final: 0.7324 (m-80) REVERT: C 61 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7690 (ppp) REVERT: C 237 ASN cc_start: 0.7862 (t0) cc_final: 0.7619 (t0) REVERT: C 241 PHE cc_start: 0.6998 (p90) cc_final: 0.6708 (p90) REVERT: C 290 ASP cc_start: 0.5652 (p0) cc_final: 0.5396 (p0) REVERT: E 6 GLU cc_start: 0.7586 (pm20) cc_final: 0.7120 (pm20) REVERT: E 19 LYS cc_start: 0.8298 (tttp) cc_final: 0.8038 (ptmm) REVERT: E 46 GLU cc_start: 0.7345 (pt0) cc_final: 0.7047 (pp20) REVERT: E 140 MET cc_start: 0.5144 (mpp) cc_final: 0.4513 (mpp) REVERT: E 153 GLU cc_start: 0.5023 (OUTLIER) cc_final: 0.3173 (pp20) REVERT: E 192 MET cc_start: 0.6429 (ttp) cc_final: 0.5274 (tpp) outliers start: 46 outliers final: 25 residues processed: 189 average time/residue: 0.9540 time to fit residues: 194.4450 Evaluate side-chains 169 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 88 optimal weight: 7.9990 chunk 3 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.202737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.148753 restraints weight = 10570.062| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.92 r_work: 0.3673 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8610 Z= 0.118 Angle : 0.614 12.351 11728 Z= 0.316 Chirality : 0.042 0.152 1386 Planarity : 0.003 0.036 1490 Dihedral : 5.267 37.064 1221 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.43 % Allowed : 24.15 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.24), residues: 1121 helix: -1.58 (0.27), residues: 326 sheet: -0.92 (0.29), residues: 274 loop : -1.54 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.005 0.001 HIS C 311 PHE 0.012 0.001 PHE B 334 TYR 0.010 0.001 TYR E 190 ARG 0.007 0.000 ARG E 18 Details of bonding type rmsd link_TRANS : bond 0.00064 ( 1) link_TRANS : angle 0.16106 ( 3) hydrogen bonds : bond 0.03029 ( 286) hydrogen bonds : angle 5.26348 ( 792) SS BOND : bond 0.00290 ( 4) SS BOND : angle 0.82646 ( 8) covalent geometry : bond 0.00270 ( 8605) covalent geometry : angle 0.61374 (11717) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7800 (m) REVERT: B 14 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: B 21 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8249 (ttp80) REVERT: B 297 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7720 (mp0) REVERT: B 326 SER cc_start: 0.8922 (m) cc_final: 0.8644 (p) REVERT: C 61 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7680 (ppp) REVERT: C 243 THR cc_start: 0.8109 (p) cc_final: 0.7863 (p) REVERT: C 290 ASP cc_start: 0.5459 (p0) cc_final: 0.5171 (p0) REVERT: E 6 GLU cc_start: 0.7547 (pm20) cc_final: 0.7118 (pm20) REVERT: E 19 LYS cc_start: 0.8314 (tttp) cc_final: 0.8036 (ptmm) REVERT: E 46 GLU cc_start: 0.7272 (pt0) cc_final: 0.6999 (pp20) REVERT: E 140 MET cc_start: 0.4788 (mpp) cc_final: 0.4531 (mpp) REVERT: E 192 MET cc_start: 0.6258 (ttp) cc_final: 0.5115 (tpp) outliers start: 38 outliers final: 23 residues processed: 178 average time/residue: 1.3684 time to fit residues: 261.4556 Evaluate side-chains 163 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 0.0870 chunk 64 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 30.0000 chunk 45 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 overall best weight: 1.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 308 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.197616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.145947 restraints weight = 10719.255| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.93 r_work: 0.3581 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 8610 Z= 0.193 Angle : 0.673 12.394 11728 Z= 0.347 Chirality : 0.045 0.154 1386 Planarity : 0.004 0.042 1490 Dihedral : 5.453 36.512 1221 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.37 % Allowed : 23.45 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.24), residues: 1121 helix: -1.51 (0.27), residues: 325 sheet: -0.84 (0.29), residues: 277 loop : -1.54 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 36 HIS 0.003 0.001 HIS E 35 PHE 0.033 0.002 PHE C 241 TYR 0.013 0.002 TYR E 103 ARG 0.008 0.000 ARG E 18 Details of bonding type rmsd link_TRANS : bond 0.00092 ( 1) link_TRANS : angle 0.14721 ( 3) hydrogen bonds : bond 0.03385 ( 286) hydrogen bonds : angle 5.33082 ( 792) SS BOND : bond 0.00410 ( 4) SS BOND : angle 1.03623 ( 8) covalent geometry : bond 0.00457 ( 8605) covalent geometry : angle 0.67290 (11717) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7937 (m) REVERT: B 14 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7424 (tp30) REVERT: B 297 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7823 (mp0) REVERT: B 326 SER cc_start: 0.8939 (m) cc_final: 0.8667 (p) REVERT: C 44 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6429 (tp-100) REVERT: C 59 TYR cc_start: 0.7540 (m-80) cc_final: 0.7233 (m-80) REVERT: C 130 GLU cc_start: 0.7981 (mp0) cc_final: 0.7710 (mm-30) REVERT: C 243 THR cc_start: 0.7853 (p) cc_final: 0.7637 (p) REVERT: C 290 ASP cc_start: 0.5512 (p0) cc_final: 0.5302 (p0) REVERT: E 6 GLU cc_start: 0.7571 (pm20) cc_final: 0.7102 (pm20) REVERT: E 19 LYS cc_start: 0.8294 (tttp) cc_final: 0.8017 (ptmm) REVERT: E 140 MET cc_start: 0.4841 (mpp) cc_final: 0.4496 (mpp) REVERT: E 153 GLU cc_start: 0.5172 (OUTLIER) cc_final: 0.3426 (pp20) REVERT: E 192 MET cc_start: 0.6581 (ttp) cc_final: 0.5354 (tpp) outliers start: 46 outliers final: 27 residues processed: 178 average time/residue: 1.3051 time to fit residues: 256.8846 Evaluate side-chains 165 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 111 optimal weight: 0.0370 chunk 16 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN B 52 GLN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS C 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.200219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.142844 restraints weight = 10745.021| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.79 r_work: 0.3641 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8610 Z= 0.135 Angle : 0.638 12.974 11728 Z= 0.327 Chirality : 0.043 0.168 1386 Planarity : 0.004 0.043 1490 Dihedral : 5.316 35.582 1221 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.32 % Allowed : 25.44 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.24), residues: 1121 helix: -1.22 (0.28), residues: 319 sheet: -0.77 (0.30), residues: 270 loop : -1.45 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS C 311 PHE 0.011 0.001 PHE B 189 TYR 0.010 0.001 TYR C 59 ARG 0.009 0.000 ARG E 18 Details of bonding type rmsd link_TRANS : bond 0.00053 ( 1) link_TRANS : angle 0.18519 ( 3) hydrogen bonds : bond 0.03020 ( 286) hydrogen bonds : angle 5.16826 ( 792) SS BOND : bond 0.00316 ( 4) SS BOND : angle 0.92289 ( 8) covalent geometry : bond 0.00318 ( 8605) covalent geometry : angle 0.63830 (11717) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7863 (m) REVERT: B 14 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7315 (tp30) REVERT: B 297 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7798 (mp0) REVERT: B 326 SER cc_start: 0.8901 (m) cc_final: 0.8634 (p) REVERT: C 59 TYR cc_start: 0.7388 (m-80) cc_final: 0.6550 (m-80) REVERT: C 61 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7681 (ppp) REVERT: C 130 GLU cc_start: 0.7877 (mp0) cc_final: 0.7616 (mm-30) REVERT: E 6 GLU cc_start: 0.7592 (pm20) cc_final: 0.7155 (pm20) REVERT: E 19 LYS cc_start: 0.8281 (tttp) cc_final: 0.7980 (ptmm) REVERT: E 46 GLU cc_start: 0.7307 (pt0) cc_final: 0.7042 (pp20) REVERT: E 140 MET cc_start: 0.4724 (mpp) cc_final: 0.4265 (mpp) REVERT: E 153 GLU cc_start: 0.5192 (OUTLIER) cc_final: 0.3432 (pp20) REVERT: E 192 MET cc_start: 0.6448 (ttp) cc_final: 0.5292 (tpp) outliers start: 37 outliers final: 24 residues processed: 175 average time/residue: 1.0000 time to fit residues: 189.1553 Evaluate side-chains 164 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 70 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.193644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.138019 restraints weight = 10813.263| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.21 r_work: 0.3530 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 8610 Z= 0.298 Angle : 0.760 12.730 11728 Z= 0.393 Chirality : 0.049 0.199 1386 Planarity : 0.005 0.055 1490 Dihedral : 5.788 35.418 1221 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.90 % Allowed : 24.27 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.24), residues: 1121 helix: -1.46 (0.27), residues: 332 sheet: -0.91 (0.29), residues: 280 loop : -1.43 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 36 HIS 0.007 0.002 HIS C 311 PHE 0.033 0.003 PHE C 241 TYR 0.019 0.002 TYR C 59 ARG 0.011 0.001 ARG E 18 Details of bonding type rmsd link_TRANS : bond 0.00143 ( 1) link_TRANS : angle 0.21034 ( 3) hydrogen bonds : bond 0.03860 ( 286) hydrogen bonds : angle 5.54958 ( 792) SS BOND : bond 0.00515 ( 4) SS BOND : angle 1.39892 ( 8) covalent geometry : bond 0.00711 ( 8605) covalent geometry : angle 0.75904 (11717) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 209 ILE cc_start: 0.8341 (tp) cc_final: 0.8094 (tt) REVERT: B 14 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7474 (tp30) REVERT: B 21 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8244 (ptt-90) REVERT: B 35 LYS cc_start: 0.8082 (mtmm) cc_final: 0.7672 (mtpt) REVERT: B 297 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7861 (mp0) REVERT: B 309 ASP cc_start: 0.7773 (t70) cc_final: 0.7362 (t0) REVERT: B 326 SER cc_start: 0.8938 (m) cc_final: 0.8666 (p) REVERT: C 59 TYR cc_start: 0.7786 (m-80) cc_final: 0.7334 (m-80) REVERT: C 130 GLU cc_start: 0.8077 (mp0) cc_final: 0.7782 (mm-30) REVERT: E 6 GLU cc_start: 0.7585 (pm20) cc_final: 0.7124 (pm20) REVERT: E 19 LYS cc_start: 0.8287 (tttp) cc_final: 0.7991 (ptmm) REVERT: E 46 GLU cc_start: 0.7382 (pt0) cc_final: 0.7049 (pp20) REVERT: E 140 MET cc_start: 0.4842 (mpp) cc_final: 0.4402 (mpp) REVERT: E 153 GLU cc_start: 0.5011 (OUTLIER) cc_final: 0.3286 (pp20) outliers start: 42 outliers final: 25 residues processed: 177 average time/residue: 0.9196 time to fit residues: 176.0361 Evaluate side-chains 169 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 47 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.200235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143235 restraints weight = 10703.992| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.73 r_work: 0.3639 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8610 Z= 0.130 Angle : 0.657 13.258 11728 Z= 0.335 Chirality : 0.043 0.163 1386 Planarity : 0.004 0.043 1490 Dihedral : 5.378 33.791 1221 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.92 % Allowed : 26.84 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.24), residues: 1121 helix: -1.11 (0.28), residues: 326 sheet: -0.88 (0.29), residues: 275 loop : -1.32 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 99 HIS 0.004 0.001 HIS C 311 PHE 0.012 0.001 PHE B 189 TYR 0.013 0.001 TYR E 190 ARG 0.009 0.000 ARG E 18 Details of bonding type rmsd link_TRANS : bond 0.00059 ( 1) link_TRANS : angle 0.20410 ( 3) hydrogen bonds : bond 0.03015 ( 286) hydrogen bonds : angle 5.20555 ( 792) SS BOND : bond 0.00402 ( 4) SS BOND : angle 0.72557 ( 8) covalent geometry : bond 0.00308 ( 8605) covalent geometry : angle 0.65658 (11717) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ILE cc_start: 0.8213 (tp) cc_final: 0.7886 (tt) REVERT: B 297 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7881 (mp0) REVERT: B 309 ASP cc_start: 0.7615 (t70) cc_final: 0.7212 (t0) REVERT: B 326 SER cc_start: 0.8893 (m) cc_final: 0.8641 (p) REVERT: C 59 TYR cc_start: 0.7438 (m-80) cc_final: 0.6946 (m-80) REVERT: C 61 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7692 (ppp) REVERT: C 214 ARG cc_start: 0.7451 (mtm180) cc_final: 0.7057 (mtm180) REVERT: C 243 THR cc_start: 0.7719 (p) cc_final: 0.7498 (p) REVERT: E 6 GLU cc_start: 0.7589 (pm20) cc_final: 0.7159 (pm20) REVERT: E 18 ARG cc_start: 0.6652 (tpt-90) cc_final: 0.5850 (ttt90) REVERT: E 19 LYS cc_start: 0.8263 (tttp) cc_final: 0.7941 (ptmm) REVERT: E 46 GLU cc_start: 0.7259 (pt0) cc_final: 0.6958 (pp20) REVERT: E 140 MET cc_start: 0.4727 (mpp) cc_final: 0.4343 (mpp) outliers start: 25 outliers final: 19 residues processed: 168 average time/residue: 0.9434 time to fit residues: 170.9052 Evaluate side-chains 153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.202195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.147659 restraints weight = 10731.577| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.01 r_work: 0.3647 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8610 Z= 0.124 Angle : 0.660 13.728 11728 Z= 0.330 Chirality : 0.043 0.160 1386 Planarity : 0.003 0.041 1490 Dihedral : 5.238 34.176 1221 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.92 % Allowed : 27.07 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.25), residues: 1121 helix: -1.02 (0.28), residues: 332 sheet: -0.85 (0.29), residues: 277 loop : -1.25 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS C 311 PHE 0.039 0.001 PHE C 241 TYR 0.009 0.001 TYR E 103 ARG 0.009 0.000 ARG E 18 Details of bonding type rmsd link_TRANS : bond 0.00033 ( 1) link_TRANS : angle 0.19486 ( 3) hydrogen bonds : bond 0.02954 ( 286) hydrogen bonds : angle 5.07633 ( 792) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.71460 ( 8) covalent geometry : bond 0.00294 ( 8605) covalent geometry : angle 0.65963 (11717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7054.63 seconds wall clock time: 124 minutes 7.90 seconds (7447.90 seconds total)