Starting phenix.real_space_refine on Sat Sep 12 02:07:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w18_21503/09_2026/6w18_21503.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w18_21503/09_2026/6w18_21503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6w18_21503/09_2026/6w18_21503.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w18_21503/09_2026/6w18_21503.cif" model { file = "/net/cci-nas-00/data/ceres_data/6w18_21503/09_2026/6w18_21503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w18_21503/09_2026/6w18_21503.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w18_21503/09_2026/6w18_21503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w18_21503/09_2026/6w18_21503.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.097 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 8327 2.51 5 N 2310 2.21 5 O 2466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13151 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2624 Classifications: {'peptide': 370} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 88} Link IDs: {'PTRANS': 18, 'TRANS': 351} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 13, 'GLU:plan': 12, 'ASN:plan1': 2, 'GLN:plan1': 3, 'TYR:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 191 Chain: "B" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2405 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 156} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 553 Unresolved non-hydrogen angles: 691 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'ASP:plan': 16, 'ASN:plan1': 5, 'PHE:plan': 6, 'GLN:plan1': 5, 'ARG:plan': 17, 'GLU:plan': 20, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 307 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2592 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2415 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 972 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 12, 'TRANS': 161} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 577 Unresolved non-hydrogen dihedrals: 386 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'TYR:plan': 5, 'HIS:plan': 3, 'PHE:plan': 8, 'ASP:plan': 7, 'ARG:plan': 11, 'GLU:plan': 8, 'ASN:plan1': 6, 'GLN:plan1': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 249 Chain: "F" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1357 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 723 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 419 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 8, 'ASP:plan': 6, 'PHE:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 6, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 184 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.97, per 1000 atoms: 0.23 Number of scatterers: 13151 At special positions: 0 Unit cell: (98.0784, 142.739, 143.615, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 6 15.00 Mg 1 11.99 O 2466 8.00 N 2310 7.00 C 8327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 617.9 milliseconds 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3464 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 20 sheets defined 41.7% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.815A pdb=" N ARG A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.948A pdb=" N HIS A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.681A pdb=" N THR A 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 223 removed outlier: 3.709A pdb=" N VAL A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.582A pdb=" N SER A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 Proline residue: A 290 - end of helix removed outlier: 4.364A pdb=" N PHE A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.983A pdb=" N ALA A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 318 removed outlier: 4.059A pdb=" N SER A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 removed outlier: 4.369A pdb=" N GLY A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 354 through 366 removed outlier: 4.306A pdb=" N ARG A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET A 363 " --> pdb=" O HIS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.544A pdb=" N LEU A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 4.102A pdb=" N GLY A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 402 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 403 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 4.226A pdb=" N GLU A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.809A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 181 through 196 Processing helix chain 'B' and resid 207 through 217 Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.655A pdb=" N HIS B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.838A pdb=" N TYR B 255 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 257 No H-bonds generated for 'chain 'B' and resid 256 through 257' Processing helix chain 'B' and resid 258 through 263 removed outlier: 4.353A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.691A pdb=" N ILE B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.554A pdb=" N ARG B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.811A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 323 Processing helix chain 'B' and resid 348 through 359 removed outlier: 3.974A pdb=" N ASP B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 4.382A pdb=" N GLN B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN B 364 " --> pdb=" O ILE B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 359 through 364' Processing helix chain 'D' and resid 8 through 21 removed outlier: 3.670A pdb=" N THR D 16 " --> pdb=" O TYR D 12 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 67 through 76 removed outlier: 3.845A pdb=" N LEU D 71 " --> pdb=" O THR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 119 removed outlier: 5.417A pdb=" N LYS D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 137 removed outlier: 4.123A pdb=" N ARG D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 151 removed outlier: 3.690A pdb=" N LEU D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 204 removed outlier: 4.040A pdb=" N ARG D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 210 removed outlier: 6.126A pdb=" N ALA D 208 " --> pdb=" O ARG D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 removed outlier: 4.145A pdb=" N ASP D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 Processing helix chain 'D' and resid 252 through 255 removed outlier: 3.590A pdb=" N ARG D 255 " --> pdb=" O PRO D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 255' Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.980A pdb=" N SER D 260 " --> pdb=" O GLU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 298 removed outlier: 3.779A pdb=" N LEU D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 55 removed outlier: 3.545A pdb=" N GLU E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 48 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY E 49 " --> pdb=" O ASP E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 84 removed outlier: 3.787A pdb=" N ARG E 68 " --> pdb=" O GLY E 64 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 101 Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 126 through 150 removed outlier: 3.575A pdb=" N TYR E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 164 removed outlier: 3.550A pdb=" N THR E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 172 Processing helix chain 'F' and resid 4 through 20 removed outlier: 3.970A pdb=" N TYR F 8 " --> pdb=" O THR F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 97 removed outlier: 3.829A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 126 removed outlier: 3.627A pdb=" N MET F 126 " --> pdb=" O HIS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 166 removed outlier: 3.930A pdb=" N LEU F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE F 136 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN F 154 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG F 156 " --> pdb=" O PHE F 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 31 Processing helix chain 'G' and resid 34 through 47 Proline residue: G 41 - end of helix Processing helix chain 'G' and resid 54 through 60 removed outlier: 3.974A pdb=" N THR G 58 " --> pdb=" O GLN G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 86 Processing helix chain 'G' and resid 92 through 98 Processing helix chain 'G' and resid 100 through 115 Processing helix chain 'G' and resid 123 through 137 Processing helix chain 'G' and resid 140 through 147 removed outlier: 3.660A pdb=" N ASN G 147 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 4.342A pdb=" N PHE A 31 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 19 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 29 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.534A pdb=" N PHE A 75 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.859A pdb=" N ARG A 95 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201 removed outlier: 3.566A pdb=" N VAL A 183 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 181 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N THR A 182 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER A 333 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 184 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 7 through 9 removed outlier: 3.559A pdb=" N VAL B 7 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B 16 " --> pdb=" O ASP B 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 105 through 107 removed outlier: 6.756A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AA8, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AA9, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.525A pdb=" N ARG B 238 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 250 " --> pdb=" O ARG B 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.568A pdb=" N THR C 28 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 36 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL C 35 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR C 50 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU C 37 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 62 removed outlier: 4.155A pdb=" N CYS C 60 " --> pdb=" O CYS C 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 108 removed outlier: 3.802A pdb=" N PHE C 105 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS C 127 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER C 125 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.551A pdb=" N TYR C 202 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 211 through 212 Processing sheet with id=AB7, first strand: chain 'C' and resid 265 through 267 removed outlier: 3.855A pdb=" N ALA C 267 " --> pdb=" O ILE C 275 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 347 through 352 removed outlier: 4.982A pdb=" N SER C 366 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU C 350 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C 364 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY C 367 " --> pdb=" O ARG C 371 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.635A pdb=" N SER D 42 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 157 through 159 removed outlier: 3.690A pdb=" N MET D 157 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 169 " --> pdb=" O MET D 157 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL D 168 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL D 179 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP D 170 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR D 177 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 241 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 242 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 51 through 53 removed outlier: 3.639A pdb=" N SER F 73 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU F 64 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE F 72 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 74 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4448 1.34 - 1.46: 2957 1.46 - 1.58: 5940 1.58 - 1.69: 10 1.69 - 1.81: 64 Bond restraints: 13419 Sorted by residual: bond pdb=" O5' ATP A 501 " pdb=" PA ATP A 501 " ideal model delta sigma weight residual 1.579 1.604 -0.025 1.10e-02 8.26e+03 5.14e+00 bond pdb=" O5' ATP B 401 " pdb=" PA ATP B 401 " ideal model delta sigma weight residual 1.579 1.603 -0.024 1.10e-02 8.26e+03 4.90e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" O2B ATP B 401 " pdb=" PB ATP B 401 " ideal model delta sigma weight residual 1.529 1.493 0.036 2.20e-02 2.07e+03 2.70e+00 bond pdb=" O2B ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 1.529 1.493 0.036 2.20e-02 2.07e+03 2.63e+00 ... (remaining 13414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 18108 1.45 - 2.90: 155 2.90 - 4.35: 63 4.35 - 5.80: 5 5.80 - 7.25: 2 Bond angle restraints: 18333 Sorted by residual: angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 132.62 7.25 1.00e+00 1.00e+00 5.25e+01 angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 132.69 7.18 1.00e+00 1.00e+00 5.16e+01 angle pdb=" PA ATP B 401 " pdb=" O3A ATP B 401 " pdb=" PB ATP B 401 " ideal model delta sigma weight residual 136.83 132.51 4.32 1.00e+00 1.00e+00 1.86e+01 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 132.58 4.25 1.00e+00 1.00e+00 1.80e+01 angle pdb=" N VAL F 38 " pdb=" CA VAL F 38 " pdb=" C VAL F 38 " ideal model delta sigma weight residual 113.47 109.82 3.65 1.01e+00 9.80e-01 1.31e+01 ... (remaining 18328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 7431 17.45 - 34.90: 366 34.90 - 52.35: 68 52.35 - 69.81: 7 69.81 - 87.26: 6 Dihedral angle restraints: 7878 sinusoidal: 2531 harmonic: 5347 Sorted by residual: dihedral pdb=" CB GLU C 16 " pdb=" CG GLU C 16 " pdb=" CD GLU C 16 " pdb=" OE1 GLU C 16 " ideal model delta sinusoidal sigma weight residual 0.00 87.26 -87.26 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB MET F 149 " pdb=" CG MET F 149 " pdb=" SD MET F 149 " pdb=" CE MET F 149 " ideal model delta sinusoidal sigma weight residual 60.00 119.04 -59.04 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 363 " pdb=" CG MET A 363 " pdb=" SD MET A 363 " pdb=" CE MET A 363 " ideal model delta sinusoidal sigma weight residual 180.00 -129.53 -50.47 3 1.50e+01 4.44e-03 8.90e+00 ... (remaining 7875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1445 0.032 - 0.063: 422 0.063 - 0.095: 133 0.095 - 0.126: 112 0.126 - 0.158: 4 Chirality restraints: 2116 Sorted by residual: chirality pdb=" C3' ATP B 401 " pdb=" C2' ATP B 401 " pdb=" C4' ATP B 401 " pdb=" O3' ATP B 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.79 0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" C3' ATP A 501 " pdb=" C2' ATP A 501 " pdb=" C4' ATP A 501 " pdb=" O3' ATP A 501 " both_signs ideal model delta sigma weight residual False -2.63 -2.79 0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" C2' ATP A 501 " pdb=" C1' ATP A 501 " pdb=" C3' ATP A 501 " pdb=" O2' ATP A 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.54 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 2113 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 155 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO C 156 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 307 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO A 308 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 322 " 0.006 2.00e-02 2.50e+03 6.70e-03 7.85e-01 pdb=" CG PHE B 322 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE B 322 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 322 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 322 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 322 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 322 " 0.001 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 909 2.74 - 3.28: 13463 3.28 - 3.82: 19747 3.82 - 4.36: 21410 4.36 - 4.90: 38550 Nonbonded interactions: 94079 Sorted by model distance: nonbonded pdb=" O LEU B 229 " pdb=" OG1 THR B 233 " model vdw 2.196 3.040 nonbonded pdb=" NH1 ARG C 146 " pdb=" OH TYR C 171 " model vdw 2.211 3.120 nonbonded pdb=" OE1 GLU F 24 " pdb=" ND2 ASN F 120 " model vdw 2.262 3.120 nonbonded pdb=" O THR A 14 " pdb=" O3G ATP A 501 " model vdw 2.267 3.040 nonbonded pdb=" O GLU D 247 " pdb=" OG1 THR D 251 " model vdw 2.273 3.040 ... (remaining 94074 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.450 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 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 : 0.002 0.036 13419 Z= 0.099 Angle : 0.412 7.246 18333 Z= 0.245 Chirality : 0.040 0.158 2116 Planarity : 0.002 0.042 2404 Dihedral : 11.010 87.256 4414 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.18), residues: 1807 helix: -0.42 (0.20), residues: 634 sheet: -3.42 (0.27), residues: 221 loop : -3.44 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 42 TYR 0.003 0.000 TYR A 246 PHE 0.015 0.000 PHE B 322 TRP 0.002 0.000 TRP C 45 HIS 0.001 0.000 HIS C 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.10 (13419) covalent geometry : angle 0.41157 / 0.25 (18333) hydrogen bonds : bond 0.16797 / 10.59 ( 524) hydrogen bonds : angle 6.57944 / 4.61 ( 1467) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 THR cc_start: 0.8468 (p) cc_final: 0.8264 (p) REVERT: A 362 GLU cc_start: 0.7101 (tt0) cc_final: 0.6668 (mm-30) REVERT: A 373 ASP cc_start: 0.5645 (m-30) cc_final: 0.5159 (t0) REVERT: A 408 ASP cc_start: 0.5975 (m-30) cc_final: 0.5640 (t0) REVERT: B 19 TYR cc_start: 0.4779 (m-10) cc_final: 0.4295 (t80) REVERT: B 87 ASP cc_start: 0.6840 (t0) cc_final: 0.5821 (m-30) REVERT: B 165 VAL cc_start: 0.7147 (t) cc_final: 0.6930 (m) REVERT: B 229 LEU cc_start: 0.8602 (mp) cc_final: 0.8212 (tp) REVERT: B 363 GLN cc_start: 0.6565 (pm20) cc_final: 0.6058 (mp10) REVERT: C 8 HIS cc_start: 0.5463 (m170) cc_final: 0.5148 (m-70) REVERT: C 9 ILE cc_start: 0.7652 (mm) cc_final: 0.7397 (pt) REVERT: D 1 MET cc_start: 0.5289 (ptp) cc_final: 0.4974 (ptt) REVERT: D 27 ILE cc_start: 0.7818 (mt) cc_final: 0.6963 (mp) REVERT: D 84 MET cc_start: 0.5121 (pmm) cc_final: 0.4892 (pmm) REVERT: D 161 TYR cc_start: 0.7362 (p90) cc_final: 0.7104 (p90) REVERT: D 257 ASP cc_start: 0.7059 (p0) cc_final: 0.6852 (p0) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.1182 time to fit residues: 62.8087 Evaluate side-chains 201 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 ASN A 379 HIS B 327 HIS C 239 GLN C 278 GLN C 343 HIS D 124 HIS D 160 HIS D 249 HIS ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.169424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.154954 restraints weight = 26406.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.155361 restraints weight = 31927.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.155180 restraints weight = 26536.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.155152 restraints weight = 21362.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.155816 restraints weight = 18867.018| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13419 Z= 0.140 Angle : 0.567 5.792 18333 Z= 0.298 Chirality : 0.046 0.206 2116 Planarity : 0.004 0.051 2404 Dihedral : 3.689 67.742 1959 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.27 % Allowed : 5.05 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.19), residues: 1807 helix: 0.51 (0.21), residues: 633 sheet: -2.66 (0.30), residues: 228 loop : -2.64 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 146 TYR 0.016 0.001 TYR B 255 PHE 0.026 0.002 PHE D 265 TRP 0.011 0.001 TRP A 387 HIS 0.007 0.001 HIS D 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (13419) covalent geometry : angle 0.56728 / 0.30 (18333) hydrogen bonds : bond 0.03400 / 2.12 ( 524) hydrogen bonds : angle 4.58303 / 3.26 ( 1467) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 267 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 THR cc_start: 0.8480 (p) cc_final: 0.8186 (p) REVERT: A 373 ASP cc_start: 0.5622 (m-30) cc_final: 0.5007 (t0) REVERT: A 408 ASP cc_start: 0.6422 (m-30) cc_final: 0.6109 (m-30) REVERT: B 71 MET cc_start: 0.4765 (mtp) cc_final: 0.2683 (tpt) REVERT: B 87 ASP cc_start: 0.6520 (t0) cc_final: 0.5494 (m-30) REVERT: B 165 VAL cc_start: 0.7535 (t) cc_final: 0.7284 (m) REVERT: B 363 GLN cc_start: 0.6941 (pm20) cc_final: 0.6366 (mp10) REVERT: D 257 ASP cc_start: 0.7119 (p0) cc_final: 0.6837 (p0) REVERT: D 280 MET cc_start: 0.7417 (mmm) cc_final: 0.6134 (mmm) REVERT: F 159 LEU cc_start: 0.8974 (tp) cc_final: 0.8654 (tp) outliers start: 3 outliers final: 1 residues processed: 270 average time/residue: 0.1102 time to fit residues: 43.8812 Evaluate side-chains 181 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 30 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 92 optimal weight: 0.0050 chunk 86 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 overall best weight: 3.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN A 404 HIS B 265 HIS C 133 ASN C 278 GLN D 160 HIS ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.152681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135070 restraints weight = 27521.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134141 restraints weight = 32837.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.134519 restraints weight = 31412.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133058 restraints weight = 22468.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133583 restraints weight = 20744.095| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13419 Z= 0.226 Angle : 0.700 7.705 18333 Z= 0.369 Chirality : 0.049 0.213 2116 Planarity : 0.005 0.055 2404 Dihedral : 4.963 77.226 1959 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.53 % Allowed : 6.55 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.19), residues: 1807 helix: 0.05 (0.21), residues: 649 sheet: -2.52 (0.31), residues: 233 loop : -2.74 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 195 TYR 0.017 0.002 TYR C 233 PHE 0.034 0.003 PHE C 115 TRP 0.031 0.003 TRP A 109 HIS 0.012 0.002 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.23 (13419) covalent geometry : angle 0.70016 / 0.37 (18333) hydrogen bonds : bond 0.04569 / 2.96 ( 524) hydrogen bonds : angle 5.16631 / 3.67 ( 1467) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 220 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 GLN cc_start: 0.7972 (mp10) cc_final: 0.7678 (mp10) REVERT: A 408 ASP cc_start: 0.6856 (m-30) cc_final: 0.6556 (m-30) REVERT: B 165 VAL cc_start: 0.8281 (t) cc_final: 0.7770 (m) REVERT: B 363 GLN cc_start: 0.7379 (pm20) cc_final: 0.6645 (mp10) REVERT: B 380 ARG cc_start: 0.7092 (mmp80) cc_final: 0.6768 (mmp80) REVERT: C 346 MET cc_start: 0.7903 (ttt) cc_final: 0.7575 (ttt) REVERT: D 82 PRO cc_start: 0.7478 (Cg_exo) cc_final: 0.7188 (Cg_endo) REVERT: D 163 ASP cc_start: 0.7519 (p0) cc_final: 0.7272 (p0) REVERT: D 257 ASP cc_start: 0.7583 (p0) cc_final: 0.7234 (p0) outliers start: 6 outliers final: 4 residues processed: 225 average time/residue: 0.1059 time to fit residues: 35.5588 Evaluate side-chains 160 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 96 optimal weight: 0.0060 chunk 172 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 HIS C 278 GLN D 160 HIS D 263 GLN E 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.153936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.134717 restraints weight = 27265.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133888 restraints weight = 34236.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135545 restraints weight = 29360.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.135073 restraints weight = 21100.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135438 restraints weight = 17728.173| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13419 Z= 0.170 Angle : 0.615 8.738 18333 Z= 0.324 Chirality : 0.046 0.165 2116 Planarity : 0.004 0.052 2404 Dihedral : 4.731 86.073 1959 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.09 % Allowed : 4.07 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.20), residues: 1807 helix: 0.37 (0.21), residues: 637 sheet: -2.34 (0.32), residues: 231 loop : -2.41 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 210 TYR 0.015 0.002 TYR F 121 PHE 0.021 0.002 PHE B 322 TRP 0.020 0.002 TRP A 387 HIS 0.012 0.002 HIS C 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (13419) covalent geometry : angle 0.61531 / 0.32 (18333) hydrogen bonds : bond 0.03911 / 2.50 ( 524) hydrogen bonds : angle 4.90317 / 3.48 ( 1467) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.6067 (tmtt) cc_final: 0.5772 (tmtt) REVERT: A 316 GLN cc_start: 0.7948 (mp10) cc_final: 0.7742 (mp10) REVERT: A 408 ASP cc_start: 0.7095 (m-30) cc_final: 0.6751 (m-30) REVERT: B 363 GLN cc_start: 0.7254 (pm20) cc_final: 0.6528 (mp10) REVERT: C 173 LEU cc_start: 0.8590 (mm) cc_final: 0.8375 (mm) REVERT: D 257 ASP cc_start: 0.7626 (p0) cc_final: 0.7320 (p0) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.1119 time to fit residues: 34.5652 Evaluate side-chains 161 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 135 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 169 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 overall best weight: 0.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 348 HIS D 160 HIS ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.158529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.139580 restraints weight = 27224.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.138667 restraints weight = 37263.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.140514 restraints weight = 29090.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.140438 restraints weight = 19493.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.140914 restraints weight = 17708.194| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13419 Z= 0.106 Angle : 0.554 9.336 18333 Z= 0.282 Chirality : 0.044 0.167 2116 Planarity : 0.004 0.063 2404 Dihedral : 4.313 88.508 1959 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.20), residues: 1807 helix: 0.62 (0.22), residues: 649 sheet: -2.01 (0.32), residues: 237 loop : -2.26 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 195 TYR 0.025 0.001 TYR B 188 PHE 0.016 0.001 PHE A 147 TRP 0.019 0.001 TRP A 387 HIS 0.017 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (13419) covalent geometry : angle 0.55417 / 0.28 (18333) hydrogen bonds : bond 0.03109 / 1.99 ( 524) hydrogen bonds : angle 4.50304 / 3.20 ( 1467) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.7076 (m-10) cc_final: 0.6254 (t80) REVERT: A 169 TRP cc_start: 0.8601 (m-10) cc_final: 0.7855 (m-10) REVERT: A 287 PHE cc_start: 0.6984 (m-80) cc_final: 0.6699 (m-80) REVERT: A 337 THR cc_start: 0.8466 (p) cc_final: 0.8264 (p) REVERT: A 408 ASP cc_start: 0.7050 (m-30) cc_final: 0.6694 (m-30) REVERT: B 165 VAL cc_start: 0.8171 (t) cc_final: 0.7871 (p) REVERT: B 363 GLN cc_start: 0.7104 (pm20) cc_final: 0.6466 (mp10) REVERT: C 226 ASP cc_start: 0.8299 (p0) cc_final: 0.8053 (p0) REVERT: C 346 MET cc_start: 0.7876 (ttt) cc_final: 0.7607 (ttt) REVERT: D 82 PRO cc_start: 0.7788 (Cg_exo) cc_final: 0.7445 (Cg_endo) REVERT: D 257 ASP cc_start: 0.7640 (p0) cc_final: 0.7277 (p0) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1127 time to fit residues: 37.0951 Evaluate side-chains 165 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 126 optimal weight: 0.9980 chunk 93 optimal weight: 0.0570 chunk 130 optimal weight: 0.5980 chunk 150 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 overall best weight: 1.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN B 348 HIS C 47 HIS D 160 HIS E 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.154521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.135745 restraints weight = 27070.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135024 restraints weight = 34566.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136223 restraints weight = 29361.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.136451 restraints weight = 22578.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.136961 restraints weight = 19228.487| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13419 Z= 0.146 Angle : 0.591 8.783 18333 Z= 0.307 Chirality : 0.045 0.160 2116 Planarity : 0.004 0.053 2404 Dihedral : 4.526 88.938 1959 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.20), residues: 1807 helix: 0.63 (0.22), residues: 645 sheet: -2.11 (0.32), residues: 242 loop : -2.17 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 195 TYR 0.024 0.001 TYR B 188 PHE 0.019 0.002 PHE B 322 TRP 0.013 0.001 TRP A 387 HIS 0.010 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (13419) covalent geometry : angle 0.59060 / 0.31 (18333) hydrogen bonds : bond 0.03606 / 2.30 ( 524) hydrogen bonds : angle 4.63021 / 3.30 ( 1467) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.6052 (tmtt) cc_final: 0.5635 (tmtt) REVERT: A 88 TYR cc_start: 0.7119 (m-10) cc_final: 0.6300 (t80) REVERT: A 105 MET cc_start: 0.8694 (tpp) cc_final: 0.8419 (tpp) REVERT: A 169 TRP cc_start: 0.8568 (m-10) cc_final: 0.7699 (m-10) REVERT: A 248 CYS cc_start: 0.7843 (p) cc_final: 0.7628 (p) REVERT: A 287 PHE cc_start: 0.7234 (m-80) cc_final: 0.6880 (m-80) REVERT: A 408 ASP cc_start: 0.7239 (m-30) cc_final: 0.6871 (m-30) REVERT: B 165 VAL cc_start: 0.8299 (t) cc_final: 0.8083 (p) REVERT: B 363 GLN cc_start: 0.7234 (pm20) cc_final: 0.6609 (mp10) REVERT: D 82 PRO cc_start: 0.7894 (Cg_exo) cc_final: 0.7586 (Cg_endo) REVERT: D 109 MET cc_start: 0.9380 (mmm) cc_final: 0.9107 (mmm) REVERT: D 257 ASP cc_start: 0.7523 (p0) cc_final: 0.7142 (p0) REVERT: F 91 MET cc_start: 0.8292 (mmm) cc_final: 0.8073 (mmm) REVERT: F 159 LEU cc_start: 0.8943 (tp) cc_final: 0.8707 (tt) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.1059 time to fit residues: 32.5138 Evaluate side-chains 163 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 48 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 135 optimal weight: 30.0000 chunk 117 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN D 160 HIS D 173 HIS E 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.144532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123030 restraints weight = 28208.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122361 restraints weight = 27999.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123667 restraints weight = 24353.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124244 restraints weight = 17523.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.124551 restraints weight = 15313.850| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 13419 Z= 0.338 Angle : 0.848 12.057 18333 Z= 0.454 Chirality : 0.054 0.256 2116 Planarity : 0.006 0.059 2404 Dihedral : 6.168 87.336 1959 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 0.18 % Allowed : 2.66 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.20), residues: 1807 helix: -0.27 (0.20), residues: 651 sheet: -2.46 (0.31), residues: 259 loop : -2.50 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 71 TYR 0.024 0.003 TYR C 233 PHE 0.044 0.003 PHE A 147 TRP 0.019 0.003 TRP B 368 HIS 0.013 0.002 HIS C 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00776 / 0.34 (13419) covalent geometry : angle 0.84765 / 0.45 (18333) hydrogen bonds : bond 0.05644 / 3.68 ( 524) hydrogen bonds : angle 5.80860 / 4.11 ( 1467) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.6571 (tmtt) cc_final: 0.6368 (tmtt) REVERT: A 287 PHE cc_start: 0.7757 (m-80) cc_final: 0.7394 (m-80) REVERT: B 165 VAL cc_start: 0.8542 (t) cc_final: 0.8288 (p) REVERT: B 191 SER cc_start: 0.9118 (p) cc_final: 0.8896 (t) REVERT: B 363 GLN cc_start: 0.7604 (pm20) cc_final: 0.6937 (mp10) REVERT: D 206 ARG cc_start: 0.7672 (mpp80) cc_final: 0.7294 (mpp80) REVERT: D 257 ASP cc_start: 0.7946 (p0) cc_final: 0.7631 (p0) REVERT: D 276 SER cc_start: 0.9030 (p) cc_final: 0.8823 (t) outliers start: 2 outliers final: 1 residues processed: 181 average time/residue: 0.1080 time to fit residues: 29.4705 Evaluate side-chains 148 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 115 optimal weight: 0.0070 chunk 118 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 chunk 157 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 40 optimal weight: 0.0670 chunk 68 optimal weight: 6.9990 overall best weight: 2.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 348 HIS ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.150272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128137 restraints weight = 27394.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.127211 restraints weight = 28218.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128511 restraints weight = 23978.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128993 restraints weight = 18784.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129443 restraints weight = 15392.144| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13419 Z= 0.158 Angle : 0.640 10.517 18333 Z= 0.336 Chirality : 0.046 0.166 2116 Planarity : 0.005 0.053 2404 Dihedral : 5.131 81.670 1959 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.09 % Allowed : 1.06 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.20), residues: 1807 helix: 0.23 (0.22), residues: 643 sheet: -2.35 (0.32), residues: 244 loop : -2.25 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 23 TYR 0.017 0.002 TYR C 233 PHE 0.021 0.002 PHE B 336 TRP 0.034 0.002 TRP A 109 HIS 0.020 0.002 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (13419) covalent geometry : angle 0.64039 / 0.34 (18333) hydrogen bonds : bond 0.04100 / 2.62 ( 524) hydrogen bonds : angle 5.07769 / 3.60 ( 1467) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.6333 (tmtt) cc_final: 0.6114 (tmtt) REVERT: A 169 TRP cc_start: 0.8682 (m-10) cc_final: 0.8346 (m-10) REVERT: A 287 PHE cc_start: 0.7575 (m-80) cc_final: 0.7227 (m-80) REVERT: A 316 GLN cc_start: 0.7909 (mp10) cc_final: 0.7575 (mp10) REVERT: B 363 GLN cc_start: 0.7451 (pm20) cc_final: 0.6801 (mp10) REVERT: D 206 ARG cc_start: 0.7663 (mpp80) cc_final: 0.7251 (mpp80) REVERT: D 257 ASP cc_start: 0.7959 (p0) cc_final: 0.7554 (p0) REVERT: D 276 SER cc_start: 0.8977 (p) cc_final: 0.8732 (t) REVERT: F 91 MET cc_start: 0.8299 (mmm) cc_final: 0.8070 (mmt) REVERT: F 159 LEU cc_start: 0.8934 (tp) cc_final: 0.8655 (tp) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1097 time to fit residues: 35.0597 Evaluate side-chains 165 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 150 optimal weight: 20.0000 chunk 3 optimal weight: 0.6980 chunk 67 optimal weight: 0.0570 chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 69 optimal weight: 0.0670 chunk 40 optimal weight: 20.0000 chunk 0 optimal weight: 0.6980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN C 43 ASN D 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.155137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.135969 restraints weight = 27116.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134947 restraints weight = 35247.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136693 restraints weight = 28188.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.136898 restraints weight = 19831.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137327 restraints weight = 17854.285| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.6573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13419 Z= 0.114 Angle : 0.610 10.702 18333 Z= 0.312 Chirality : 0.045 0.179 2116 Planarity : 0.004 0.054 2404 Dihedral : 4.570 80.724 1959 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.27 % Allowed : 1.15 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.20), residues: 1807 helix: 0.63 (0.22), residues: 639 sheet: -2.14 (0.32), residues: 242 loop : -2.00 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 23 TYR 0.012 0.001 TYR D 161 PHE 0.018 0.001 PHE B 351 TRP 0.045 0.002 TRP C 284 HIS 0.017 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (13419) covalent geometry : angle 0.61023 / 0.31 (18333) hydrogen bonds : bond 0.03312 / 2.09 ( 524) hydrogen bonds : angle 4.70801 / 3.34 ( 1467) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 211 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.7031 (m-10) cc_final: 0.6013 (t80) REVERT: A 126 PHE cc_start: 0.8118 (m-80) cc_final: 0.7811 (m-10) REVERT: A 169 TRP cc_start: 0.8505 (m-10) cc_final: 0.8093 (m-10) REVERT: A 287 PHE cc_start: 0.7311 (m-80) cc_final: 0.6988 (m-80) REVERT: A 316 GLN cc_start: 0.7822 (mp10) cc_final: 0.7587 (mp10) REVERT: B 363 GLN cc_start: 0.7419 (pm20) cc_final: 0.6781 (mp10) REVERT: D 82 PRO cc_start: 0.7951 (Cg_exo) cc_final: 0.7667 (Cg_endo) REVERT: D 257 ASP cc_start: 0.7562 (p0) cc_final: 0.7033 (p0) REVERT: D 259 ILE cc_start: 0.8635 (mm) cc_final: 0.8333 (pt) REVERT: D 294 VAL cc_start: 0.7562 (t) cc_final: 0.7314 (t) outliers start: 3 outliers final: 0 residues processed: 212 average time/residue: 0.1171 time to fit residues: 36.0670 Evaluate side-chains 169 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 26 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 111 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 180 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN D 160 HIS E 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.156683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.137255 restraints weight = 27022.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.136750 restraints weight = 36196.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137856 restraints weight = 28183.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137856 restraints weight = 20769.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137856 restraints weight = 20769.996| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.6576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13419 Z= 0.110 Angle : 0.613 10.707 18333 Z= 0.312 Chirality : 0.045 0.165 2116 Planarity : 0.004 0.054 2404 Dihedral : 4.442 80.680 1959 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.27 % Allowed : 0.18 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.21), residues: 1807 helix: 0.83 (0.22), residues: 639 sheet: -2.02 (0.31), residues: 263 loop : -1.90 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 98 TYR 0.021 0.001 TYR B 221 PHE 0.015 0.001 PHE B 336 TRP 0.034 0.002 TRP C 284 HIS 0.017 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13419) covalent geometry : angle 0.61326 / 0.31 (18333) hydrogen bonds : bond 0.03243 / 2.03 ( 524) hydrogen bonds : angle 4.62704 / 3.28 ( 1467) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.7046 (m-10) cc_final: 0.5946 (t80) REVERT: A 126 PHE cc_start: 0.8035 (m-80) cc_final: 0.7728 (m-10) REVERT: A 169 TRP cc_start: 0.8362 (m-10) cc_final: 0.7888 (m-10) REVERT: A 248 CYS cc_start: 0.7917 (p) cc_final: 0.7598 (p) REVERT: A 287 PHE cc_start: 0.7210 (m-80) cc_final: 0.6898 (m-80) REVERT: A 316 GLN cc_start: 0.7703 (mp10) cc_final: 0.7466 (mp10) REVERT: B 363 GLN cc_start: 0.7431 (pm20) cc_final: 0.6847 (mp10) REVERT: D 82 PRO cc_start: 0.7936 (Cg_exo) cc_final: 0.7642 (Cg_endo) REVERT: D 257 ASP cc_start: 0.7383 (p0) cc_final: 0.6803 (p0) REVERT: D 294 VAL cc_start: 0.7479 (t) cc_final: 0.7249 (t) outliers start: 3 outliers final: 0 residues processed: 211 average time/residue: 0.1042 time to fit residues: 32.8232 Evaluate side-chains 160 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 90 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 152 optimal weight: 4.9990 chunk 109 optimal weight: 0.0980 chunk 130 optimal weight: 2.9990 chunk 32 optimal weight: 0.0370 chunk 85 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN B 265 HIS D 160 HIS E 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.154229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135171 restraints weight = 26744.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.134352 restraints weight = 36978.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.135709 restraints weight = 30720.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.136261 restraints weight = 21985.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136447 restraints weight = 19844.869| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13419 Z= 0.136 Angle : 0.631 11.203 18333 Z= 0.324 Chirality : 0.046 0.279 2116 Planarity : 0.004 0.054 2404 Dihedral : 4.644 82.415 1959 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.27 % Allowed : 0.27 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.21), residues: 1807 helix: 0.77 (0.22), residues: 640 sheet: -2.03 (0.31), residues: 262 loop : -1.83 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 23 TYR 0.018 0.001 TYR C 233 PHE 0.016 0.002 PHE B 322 TRP 0.034 0.002 TRP C 284 HIS 0.017 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (13419) covalent geometry : angle 0.63052 / 0.32 (18333) hydrogen bonds : bond 0.03519 / 2.22 ( 524) hydrogen bonds : angle 4.71961 / 3.35 ( 1467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1925.92 seconds wall clock time: 34 minutes 4.63 seconds (2044.63 seconds total)