Starting phenix.real_space_refine on Thu Jul 31 02:41:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w18_21503/07_2025/6w18_21503.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w18_21503/07_2025/6w18_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6w18_21503/07_2025/6w18_21503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w18_21503/07_2025/6w18_21503.map" model { file = "/net/cci-nas-00/data/ceres_data/6w18_21503/07_2025/6w18_21503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w18_21503/07_2025/6w18_21503.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 13} 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: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 6, 'GLU:plan': 20, 'ARG:plan': 17} 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: {'ARG:plan': 1, 'TRP: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: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 11} 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: {'GLN:plan1': 8, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 6} 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: 8.08, per 1000 atoms: 0.61 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: 4.27 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.60 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: 3.90 Time building geometry restraints manager: 4.07 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: 7454 17.45 - 34.90: 378 34.90 - 52.35: 84 52.35 - 69.81: 17 69.81 - 87.26: 7 Dihedral angle restraints: 7940 sinusoidal: 2593 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 7937 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: 1.380 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.520 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 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 : 11.721 87.256 4476 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (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 TRP 0.002 0.000 TRP C 45 HIS 0.001 0.000 HIS C 8 PHE 0.015 0.000 PHE B 322 TYR 0.003 0.000 TYR A 246 ARG 0.002 0.000 ARG F 42 Details of bonding type rmsd hydrogen bonds : bond 0.16797 ( 524) hydrogen bonds : angle 6.57944 ( 1467) covalent geometry : bond 0.00172 (13419) covalent geometry : angle 0.41157 (18333) *********************** 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 : 1.434 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: 0.5638 (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: 0.8213 (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: 0.5147 (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: 0.4959 (ptt) REVERT: D 27 ILE cc_start: 0.7818 (mt) cc_final: 0.6962 (mp) REVERT: D 84 MET cc_start: 0.5121 (pmm) cc_final: 0.4893 (pmm) REVERT: D 161 TYR cc_start: 0.7362 (p90) cc_final: 0.7102 (p90) REVERT: D 257 ASP cc_start: 0.7059 (p0) cc_final: 0.6854 (p0) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.2893 time to fit residues: 151.3222 Evaluate side-chains 202 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 73 optimal weight: 0.2980 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 379 HIS B 327 HIS ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** F 33 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.166538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.151315 restraints weight = 26464.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.150905 restraints weight = 34465.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.151085 restraints weight = 30386.742| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13419 Z= 0.173 Angle : 0.596 6.205 18333 Z= 0.316 Chirality : 0.046 0.212 2116 Planarity : 0.004 0.052 2404 Dihedral : 5.280 83.157 2021 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.18 % Allowed : 5.49 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.19), residues: 1807 helix: 0.40 (0.21), residues: 638 sheet: -2.57 (0.30), residues: 222 loop : -2.78 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 321 HIS 0.006 0.001 HIS A 379 PHE 0.035 0.002 PHE D 265 TYR 0.017 0.002 TYR B 255 ARG 0.007 0.001 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 524) hydrogen bonds : angle 4.67235 ( 1467) covalent geometry : bond 0.00359 (13419) covalent geometry : angle 0.59568 (18333) *********************** 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 262 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 260 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 THR cc_start: 0.8569 (p) cc_final: 0.8290 (p) REVERT: A 373 ASP cc_start: 0.5704 (m-30) cc_final: 0.5091 (t0) REVERT: A 408 ASP cc_start: 0.6497 (m-30) cc_final: 0.6242 (m-30) REVERT: B 71 MET cc_start: 0.4768 (mtp) cc_final: 0.4568 (ttm) REVERT: B 165 VAL cc_start: 0.7620 (t) cc_final: 0.7313 (m) REVERT: B 363 GLN cc_start: 0.7004 (pm20) cc_final: 0.6380 (mp10) REVERT: D 109 MET cc_start: 0.9160 (mmm) cc_final: 0.8915 (mmt) REVERT: F 159 LEU cc_start: 0.8996 (tp) cc_final: 0.8678 (tp) outliers start: 2 outliers final: 1 residues processed: 262 average time/residue: 0.2504 time to fit residues: 93.8962 Evaluate side-chains 178 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 151 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 24 ASN B 265 HIS C 133 ASN C 278 GLN D 160 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.161257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.143376 restraints weight = 27470.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.143269 restraints weight = 31689.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.144055 restraints weight = 27282.722| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13419 Z= 0.143 Angle : 0.568 7.278 18333 Z= 0.296 Chirality : 0.045 0.162 2116 Planarity : 0.004 0.052 2404 Dihedral : 5.025 67.869 2021 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1807 helix: 0.56 (0.21), residues: 645 sheet: -2.41 (0.32), residues: 223 loop : -2.49 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 259 HIS 0.009 0.001 HIS C 343 PHE 0.017 0.002 PHE A 31 TYR 0.012 0.002 TYR B 188 ARG 0.009 0.001 ARG B 195 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 524) hydrogen bonds : angle 4.60387 ( 1467) covalent geometry : bond 0.00320 (13419) covalent geometry : angle 0.56849 (18333) *********************** 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 232 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 THR cc_start: 0.8791 (p) cc_final: 0.8481 (p) REVERT: A 408 ASP cc_start: 0.6722 (m-30) cc_final: 0.6322 (m-30) REVERT: B 165 VAL cc_start: 0.7967 (t) cc_final: 0.7543 (m) REVERT: B 227 HIS cc_start: 0.7914 (p90) cc_final: 0.7712 (p90) REVERT: B 363 GLN cc_start: 0.7135 (pm20) cc_final: 0.6557 (mp10) REVERT: D 82 PRO cc_start: 0.7411 (Cg_exo) cc_final: 0.7177 (Cg_endo) REVERT: D 257 ASP cc_start: 0.7359 (p0) cc_final: 0.7111 (p0) REVERT: F 159 LEU cc_start: 0.8936 (tp) cc_final: 0.8635 (tp) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.2415 time to fit residues: 82.1077 Evaluate side-chains 165 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 142 optimal weight: 20.0000 chunk 175 optimal weight: 0.1980 chunk 93 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN D 249 HIS ** E 19 ASN ** 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 = 0.4157 r_free = 0.4157 target = 0.162936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.144799 restraints weight = 26416.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.143945 restraints weight = 33190.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.145604 restraints weight = 26420.895| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13419 Z= 0.103 Angle : 0.530 8.631 18333 Z= 0.272 Chirality : 0.044 0.165 2116 Planarity : 0.004 0.053 2404 Dihedral : 4.840 64.860 2021 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.20), residues: 1807 helix: 0.83 (0.22), residues: 650 sheet: -2.26 (0.32), residues: 230 loop : -2.34 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 387 HIS 0.006 0.001 HIS B 327 PHE 0.023 0.001 PHE D 250 TYR 0.013 0.001 TYR B 221 ARG 0.006 0.000 ARG B 195 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 524) hydrogen bonds : angle 4.40138 ( 1467) covalent geometry : bond 0.00224 (13419) covalent geometry : angle 0.53040 (18333) *********************** 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 232 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.429 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: A 83 LYS cc_start: 0.5953 (tmtt) cc_final: 0.5499 (tmtt) REVERT: A 337 THR cc_start: 0.8687 (p) cc_final: 0.8373 (p) REVERT: A 373 ASP cc_start: 0.5868 (m-30) cc_final: 0.5313 (t0) REVERT: A 408 ASP cc_start: 0.6796 (m-30) cc_final: 0.6323 (m-30) REVERT: B 165 VAL cc_start: 0.7961 (t) cc_final: 0.7546 (m) REVERT: B 363 GLN cc_start: 0.7138 (pm20) cc_final: 0.6586 (mp10) REVERT: C 145 LEU cc_start: 0.5829 (mt) cc_final: 0.5513 (pt) REVERT: C 173 LEU cc_start: 0.8534 (mm) cc_final: 0.8268 (mp) REVERT: D 257 ASP cc_start: 0.7269 (p0) cc_final: 0.6924 (p0) REVERT: F 34 SER cc_start: 0.8782 (t) cc_final: 0.8391 (p) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2591 time to fit residues: 85.4505 Evaluate side-chains 170 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 14 optimal weight: 30.0000 chunk 39 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 92 optimal weight: 0.0040 chunk 63 optimal weight: 8.9990 chunk 150 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 87 optimal weight: 0.0070 overall best weight: 3.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 ASN C 47 HIS ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3980 r_free = 0.3980 target = 0.149290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130777 restraints weight = 27541.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130252 restraints weight = 33564.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130945 restraints weight = 28672.092| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 13419 Z= 0.258 Angle : 0.742 7.543 18333 Z= 0.397 Chirality : 0.051 0.227 2116 Planarity : 0.005 0.058 2404 Dihedral : 6.261 77.938 2021 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 0.18 % Allowed : 5.05 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.20), residues: 1807 helix: 0.08 (0.21), residues: 656 sheet: -2.27 (0.32), residues: 224 loop : -2.59 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 189 HIS 0.012 0.002 HIS B 327 PHE 0.032 0.003 PHE A 147 TYR 0.027 0.002 TYR B 188 ARG 0.009 0.001 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 524) hydrogen bonds : angle 5.28139 ( 1467) covalent geometry : bond 0.00590 (13419) covalent geometry : angle 0.74238 (18333) *********************** 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 207 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.6335 (tmtt) cc_final: 0.5723 (tmtt) REVERT: A 287 PHE cc_start: 0.7405 (m-80) cc_final: 0.7175 (m-80) REVERT: A 408 ASP cc_start: 0.7101 (m-30) cc_final: 0.6861 (m-30) REVERT: B 363 GLN cc_start: 0.7614 (pm20) cc_final: 0.6883 (mp10) REVERT: C 59 THR cc_start: 0.8703 (m) cc_final: 0.8409 (m) REVERT: D 109 MET cc_start: 0.9419 (mmm) cc_final: 0.9210 (mmm) REVERT: D 257 ASP cc_start: 0.7463 (p0) cc_final: 0.7164 (p0) outliers start: 2 outliers final: 0 residues processed: 207 average time/residue: 0.2769 time to fit residues: 84.0586 Evaluate side-chains 154 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 100 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.154999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136054 restraints weight = 27106.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134737 restraints weight = 35452.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.136313 restraints weight = 28370.896| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13419 Z= 0.123 Angle : 0.594 10.714 18333 Z= 0.305 Chirality : 0.045 0.168 2116 Planarity : 0.004 0.073 2404 Dihedral : 5.420 71.263 2021 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.20), residues: 1807 helix: 0.60 (0.22), residues: 641 sheet: -2.16 (0.32), residues: 240 loop : -2.19 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 387 HIS 0.010 0.001 HIS B 327 PHE 0.015 0.001 PHE B 322 TYR 0.021 0.001 TYR B 188 ARG 0.005 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 524) hydrogen bonds : angle 4.65488 ( 1467) covalent geometry : bond 0.00275 (13419) covalent geometry : angle 0.59425 (18333) *********************** 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 216 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.6202 (tmtt) cc_final: 0.5560 (tmtt) REVERT: A 169 TRP cc_start: 0.8567 (m-10) cc_final: 0.7659 (m-10) REVERT: A 287 PHE cc_start: 0.7256 (m-80) cc_final: 0.6963 (m-80) REVERT: A 408 ASP cc_start: 0.7110 (m-30) cc_final: 0.6806 (m-30) REVERT: B 193 LEU cc_start: 0.8051 (mt) cc_final: 0.7489 (mp) REVERT: B 221 TYR cc_start: 0.5679 (t80) cc_final: 0.5452 (t80) REVERT: B 363 GLN cc_start: 0.7378 (pm20) cc_final: 0.6737 (mp10) REVERT: C 59 THR cc_start: 0.8567 (m) cc_final: 0.8244 (m) REVERT: C 226 ASP cc_start: 0.8408 (p0) cc_final: 0.8174 (p0) REVERT: D 257 ASP cc_start: 0.7444 (p0) cc_final: 0.7077 (p0) REVERT: F 159 LEU cc_start: 0.8884 (tp) cc_final: 0.8492 (tp) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.2620 time to fit residues: 81.1213 Evaluate side-chains 168 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 163 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 45 optimal weight: 40.0000 chunk 165 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 10 optimal weight: 0.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 HIS D 160 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.155119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.135914 restraints weight = 26962.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134508 restraints weight = 35859.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.136163 restraints weight = 31046.487| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.6042 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= 0.133 Angle : 0.590 9.202 18333 Z= 0.306 Chirality : 0.045 0.163 2116 Planarity : 0.004 0.080 2404 Dihedral : 5.403 72.006 2021 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.09 % Allowed : 2.04 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.20), residues: 1807 helix: 0.70 (0.22), residues: 647 sheet: -2.15 (0.30), residues: 264 loop : -2.13 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 109 HIS 0.018 0.001 HIS B 327 PHE 0.023 0.002 PHE A 147 TYR 0.019 0.001 TYR D 161 ARG 0.006 0.001 ARG C 107 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 524) hydrogen bonds : angle 4.61103 ( 1467) covalent geometry : bond 0.00299 (13419) covalent geometry : angle 0.58997 (18333) *********************** 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 213 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.6445 (tmtt) cc_final: 0.6159 (tmtt) REVERT: A 169 TRP cc_start: 0.8469 (m-10) cc_final: 0.8068 (m-10) REVERT: A 408 ASP cc_start: 0.7196 (m-30) cc_final: 0.6845 (m-30) REVERT: B 336 PHE cc_start: 0.5995 (t80) cc_final: 0.5692 (t80) REVERT: B 363 GLN cc_start: 0.7379 (pm20) cc_final: 0.6778 (mp10) REVERT: C 226 ASP cc_start: 0.8356 (p0) cc_final: 0.8106 (p0) REVERT: D 257 ASP cc_start: 0.7488 (p0) cc_final: 0.6995 (p0) REVERT: F 159 LEU cc_start: 0.8910 (tp) cc_final: 0.8517 (tp) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.2446 time to fit residues: 75.1725 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 : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 30.0000 chunk 162 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 HIS ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3972 r_free = 0.3972 target = 0.148316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.130016 restraints weight = 27797.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.128851 restraints weight = 36318.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129959 restraints weight = 32983.744| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.6796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13419 Z= 0.234 Angle : 0.724 9.970 18333 Z= 0.384 Chirality : 0.049 0.214 2116 Planarity : 0.005 0.071 2404 Dihedral : 6.417 82.051 2021 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 0.18 % Allowed : 1.95 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.20), residues: 1807 helix: 0.19 (0.21), residues: 658 sheet: -2.42 (0.31), residues: 258 loop : -2.35 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A 109 HIS 0.016 0.002 HIS B 327 PHE 0.026 0.002 PHE B 322 TYR 0.019 0.002 TYR B 188 ARG 0.010 0.001 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 524) hydrogen bonds : angle 5.29873 ( 1467) covalent geometry : bond 0.00534 (13419) covalent geometry : angle 0.72396 (18333) *********************** 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 203 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.6595 (tmtt) cc_final: 0.6257 (tmtt) REVERT: A 287 PHE cc_start: 0.7600 (m-80) cc_final: 0.7236 (m-80) REVERT: A 316 GLN cc_start: 0.8217 (mp10) cc_final: 0.7914 (mp10) REVERT: B 363 GLN cc_start: 0.7721 (pm20) cc_final: 0.7058 (mp10) REVERT: C 101 ARG cc_start: 0.8321 (mmp80) cc_final: 0.8109 (mmp-170) REVERT: D 206 ARG cc_start: 0.7675 (mpp80) cc_final: 0.7256 (mpp80) REVERT: D 257 ASP cc_start: 0.7676 (p0) cc_final: 0.7300 (p0) REVERT: D 276 SER cc_start: 0.9104 (p) cc_final: 0.8862 (t) outliers start: 2 outliers final: 0 residues processed: 202 average time/residue: 0.2596 time to fit residues: 76.8130 Evaluate side-chains 159 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 101 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 172 optimal weight: 0.0470 chunk 10 optimal weight: 0.0570 chunk 130 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 155 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.156824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.137246 restraints weight = 26608.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136438 restraints weight = 28245.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137513 restraints weight = 24413.922| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13419 Z= 0.109 Angle : 0.604 12.390 18333 Z= 0.304 Chirality : 0.045 0.169 2116 Planarity : 0.004 0.056 2404 Dihedral : 5.301 67.960 2021 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.09 % Allowed : 0.80 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.20), residues: 1807 helix: 0.74 (0.22), residues: 648 sheet: -2.11 (0.30), residues: 269 loop : -2.07 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 284 HIS 0.016 0.001 HIS B 327 PHE 0.020 0.001 PHE B 351 TYR 0.011 0.001 TYR B 218 ARG 0.005 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 524) hydrogen bonds : angle 4.63194 ( 1467) covalent geometry : bond 0.00229 (13419) covalent geometry : angle 0.60377 (18333) *********************** 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 229 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.558 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: A 83 LYS cc_start: 0.6433 (tmtt) cc_final: 0.6102 (tmtt) REVERT: A 169 TRP cc_start: 0.8468 (m-10) cc_final: 0.7947 (m-10) REVERT: A 287 PHE cc_start: 0.7186 (m-80) cc_final: 0.6825 (m-80) REVERT: A 316 GLN cc_start: 0.8155 (mp10) cc_final: 0.7912 (mp10) REVERT: A 373 ASP cc_start: 0.6501 (m-30) cc_final: 0.6164 (m-30) REVERT: A 408 ASP cc_start: 0.7559 (m-30) cc_final: 0.7143 (m-30) REVERT: B 363 GLN cc_start: 0.7393 (pm20) cc_final: 0.6868 (mp10) REVERT: D 82 PRO cc_start: 0.8013 (Cg_exo) cc_final: 0.7780 (Cg_endo) REVERT: D 257 ASP cc_start: 0.7513 (p0) cc_final: 0.7134 (p0) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.3093 time to fit residues: 101.7727 Evaluate side-chains 172 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 101 optimal weight: 3.9990 chunk 83 optimal weight: 0.0570 chunk 174 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS 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 = 0.4029 r_free = 0.4029 target = 0.152944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.133966 restraints weight = 27160.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132439 restraints weight = 35627.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133849 restraints weight = 29117.709| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.6681 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= 0.152 Angle : 0.636 12.046 18333 Z= 0.330 Chirality : 0.046 0.171 2116 Planarity : 0.005 0.093 2404 Dihedral : 5.600 74.056 2021 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 0.18 % Allowed : 0.09 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.21), residues: 1807 helix: 0.74 (0.22), residues: 644 sheet: -2.11 (0.31), residues: 256 loop : -1.98 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 284 HIS 0.014 0.002 HIS B 327 PHE 0.020 0.002 PHE C 26 TYR 0.019 0.002 TYR B 221 ARG 0.010 0.001 ARG C 98 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 524) hydrogen bonds : angle 4.84630 ( 1467) covalent geometry : bond 0.00346 (13419) covalent geometry : angle 0.63610 (18333) ********************** 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 212 residues out of total 1601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 210 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.6467 (tmtt) cc_final: 0.5760 (tmtt) REVERT: A 169 TRP cc_start: 0.8504 (m-10) cc_final: 0.7980 (m-10) REVERT: A 248 CYS cc_start: 0.7776 (p) cc_final: 0.7470 (p) REVERT: A 287 PHE cc_start: 0.7449 (m-80) cc_final: 0.6950 (m-80) REVERT: B 363 GLN cc_start: 0.7586 (pm20) cc_final: 0.6967 (mp10) REVERT: D 257 ASP cc_start: 0.7476 (p0) cc_final: 0.7148 (p0) outliers start: 2 outliers final: 0 residues processed: 211 average time/residue: 0.2533 time to fit residues: 76.9484 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 : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 120 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 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 = 0.4004 r_free = 0.4004 target = 0.150936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131980 restraints weight = 27343.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130036 restraints weight = 36724.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.131348 restraints weight = 30820.454| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.6921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13419 Z= 0.179 Angle : 0.666 11.729 18333 Z= 0.348 Chirality : 0.047 0.178 2116 Planarity : 0.005 0.053 2404 Dihedral : 5.966 79.056 2021 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.27 % Allowed : 0.35 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), residues: 1807 helix: 0.58 (0.22), residues: 652 sheet: -1.99 (0.31), residues: 266 loop : -2.07 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 284 HIS 0.014 0.001 HIS B 327 PHE 0.020 0.002 PHE B 322 TYR 0.019 0.002 TYR B 188 ARG 0.009 0.001 ARG F 105 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 524) hydrogen bonds : angle 5.01145 ( 1467) covalent geometry : bond 0.00410 (13419) covalent geometry : angle 0.66584 (18333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3945.36 seconds wall clock time: 70 minutes 28.28 seconds (4228.28 seconds total)