Starting phenix.real_space_refine on Sun Aug 24 08:20:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gf6_29979/08_2025/8gf6_29979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gf6_29979/08_2025/8gf6_29979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gf6_29979/08_2025/8gf6_29979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gf6_29979/08_2025/8gf6_29979.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gf6_29979/08_2025/8gf6_29979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gf6_29979/08_2025/8gf6_29979.map" } resolution = 3.1 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= -0.001 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 11465 2.51 5 N 3189 2.21 5 O 3550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18315 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3519 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 18, 'TRANS': 442} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MHS:plan-2': 1, 'AGM:plan-2': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3693 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 19, 'TRANS': 464} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MHS:plan-2': 1, 'AGM:plan-2': 1, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3148 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 420} Chain: "D" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3143 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 419} Chain: "E" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1926 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "F" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1926 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "X" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 9, 'TRANS': 110} Time building chain proxies: 3.91, per 1000 atoms: 0.21 Number of scatterers: 18315 At special positions: 0 Unit cell: (99.235, 102.58, 137.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 3550 8.00 N 3189 7.00 C 11465 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: 1.39 Conformation dependent library (CDL) restraints added in 608.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4364 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 15 sheets defined 54.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.852A pdb=" N HIS A 101 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR A 102 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL A 103 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.789A pdb=" N GLN A 109 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 139 through 153 removed outlier: 3.630A pdb=" N HIS A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.535A pdb=" N ALA A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 188' Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.533A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.550A pdb=" N SER A 229 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 253 Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.717A pdb=" N LYS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MHS A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 312 through 333 Processing helix chain 'A' and resid 354 through 371 Processing helix chain 'A' and resid 386 through 408 Processing helix chain 'A' and resid 408 through 415 Processing helix chain 'A' and resid 417 through 438 removed outlier: 3.744A pdb=" N ARG A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 459 Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.930A pdb=" N SMC A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 519 removed outlier: 3.550A pdb=" N TYR A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 512 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 533 Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.571A pdb=" N GLU A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.650A pdb=" N ILE A 567 " --> pdb=" O SER A 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.631A pdb=" N LEU B 100 " --> pdb=" O PRO B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.925A pdb=" N TRP B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 135 removed outlier: 3.675A pdb=" N LEU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 154 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.999A pdb=" N GLU B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.541A pdb=" N MET B 201 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 236 through 254 removed outlier: 3.556A pdb=" N ALA B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 269 removed outlier: 3.811A pdb=" N ALA B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.614A pdb=" N VAL B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 328 Processing helix chain 'B' and resid 345 through 352 removed outlier: 4.037A pdb=" N THR B 348 " --> pdb=" O GLN B 345 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 350 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 371 Processing helix chain 'B' and resid 386 through 408 Processing helix chain 'B' and resid 421 through 438 removed outlier: 3.943A pdb=" N LEU B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 459 removed outlier: 3.554A pdb=" N GLY B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 504 through 518 removed outlier: 4.180A pdb=" N HIS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 533 removed outlier: 3.785A pdb=" N LYS B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 554 removed outlier: 3.520A pdb=" N ILE B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 47 through 57 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 114 through 121 removed outlier: 3.674A pdb=" N ILE C 118 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 142 removed outlier: 4.328A pdb=" N THR C 128 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 149 through 156 Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 186 through 191 removed outlier: 4.217A pdb=" N LEU C 189 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN C 191 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 204 through 223 removed outlier: 3.594A pdb=" N ALA C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 241 removed outlier: 3.846A pdb=" N GLY C 237 " --> pdb=" O HIS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 261 through 276 removed outlier: 3.503A pdb=" N VAL C 265 " --> pdb=" O THR C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 296 through 320 removed outlier: 4.078A pdb=" N GLY C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 323 No H-bonds generated for 'chain 'C' and resid 321 through 323' Processing helix chain 'C' and resid 324 through 341 removed outlier: 4.162A pdb=" N LEU C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 347 Processing helix chain 'C' and resid 348 through 361 Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 405 through 418 removed outlier: 3.649A pdb=" N THR C 409 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE C 413 " --> pdb=" O THR C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 425 through 432 Processing helix chain 'D' and resid 22 through 25 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 47 through 57 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 125 through 144 removed outlier: 3.793A pdb=" N THR D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 149 through 159 removed outlier: 3.629A pdb=" N ALA D 153 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 removed outlier: 3.614A pdb=" N ASN D 182 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 removed outlier: 4.103A pdb=" N ASN D 191 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.934A pdb=" N THR D 201 " --> pdb=" O ILE D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 223 Processing helix chain 'D' and resid 228 through 241 removed outlier: 4.017A pdb=" N ARG D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.915A pdb=" N VAL D 253 " --> pdb=" O VAL D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 276 Processing helix chain 'D' and resid 296 through 320 Processing helix chain 'D' and resid 324 through 341 removed outlier: 4.687A pdb=" N LEU D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 347 removed outlier: 3.577A pdb=" N TYR D 347 " --> pdb=" O GLY D 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 344 through 347' Processing helix chain 'D' and resid 348 through 361 Processing helix chain 'D' and resid 387 through 398 Processing helix chain 'D' and resid 409 through 414 Processing helix chain 'D' and resid 420 through 425 Processing helix chain 'E' and resid 12 through 24 Processing helix chain 'E' and resid 33 through 42 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 65 through 71 Processing helix chain 'E' and resid 74 through 79 removed outlier: 3.520A pdb=" N ALA E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 removed outlier: 3.672A pdb=" N SER E 103 " --> pdb=" O PRO E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 141 removed outlier: 3.754A pdb=" N GLN E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 141 " --> pdb=" O VAL E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 213 Processing helix chain 'E' and resid 226 through 246 removed outlier: 3.574A pdb=" N ILE E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 Processing helix chain 'F' and resid 33 through 42 removed outlier: 3.686A pdb=" N GLY F 42 " --> pdb=" O THR F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 removed outlier: 4.032A pdb=" N GLY F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 71 Processing helix chain 'F' and resid 73 through 80 removed outlier: 3.995A pdb=" N ALA F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 128 through 141 removed outlier: 4.258A pdb=" N GLN F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR F 141 " --> pdb=" O VAL F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 210 removed outlier: 3.613A pdb=" N ALA F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing helix chain 'F' and resid 226 through 246 Processing helix chain 'X' and resid 23 through 34 removed outlier: 5.245A pdb=" N LYS X 29 " --> pdb=" O GLU X 25 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 96 No H-bonds generated for 'chain 'X' and resid 94 through 96' Processing helix chain 'X' and resid 97 through 109 removed outlier: 3.740A pdb=" N ARG X 102 " --> pdb=" O LYS X 98 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP X 106 " --> pdb=" O ARG X 102 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS X 107 " --> pdb=" O SER X 103 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET X 108 " --> pdb=" O VAL X 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 removed outlier: 3.529A pdb=" N TYR A 176 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.533A pdb=" N ARG B 81 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG X 42 " --> pdb=" O GLU X 91 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE X 92 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU X 15 " --> pdb=" O ARG X 116 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG X 116 " --> pdb=" O GLU X 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 181 removed outlier: 3.671A pdb=" N TYR B 176 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 8 removed outlier: 7.191A pdb=" N VAL C 5 " --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N SER C 17 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 7 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 103 removed outlier: 3.618A pdb=" N SER C 99 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER C 108 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 279 through 284 removed outlier: 5.516A pdb=" N VAL C 281 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS C 293 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 8 removed outlier: 7.813A pdb=" N VAL D 5 " --> pdb=" O SER D 17 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER D 17 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE D 7 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 101 through 102 removed outlier: 3.631A pdb=" N LYS D 101 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 279 through 284 removed outlier: 7.167A pdb=" N PHE D 291 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 83 through 88 Processing sheet with id=AB3, first strand: chain 'E' and resid 176 through 177 Processing sheet with id=AB4, first strand: chain 'F' and resid 83 through 86 Processing sheet with id=AB5, first strand: chain 'F' and resid 89 through 90 Processing sheet with id=AB6, first strand: chain 'F' and resid 177 through 179 removed outlier: 5.936A pdb=" N ILE F 183 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS F 187 " --> pdb=" O ARG F 196 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ARG F 196 " --> pdb=" O LYS F 187 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5378 1.33 - 1.45: 3635 1.45 - 1.58: 9449 1.58 - 1.70: 0 1.70 - 1.82: 195 Bond restraints: 18657 Sorted by residual: bond pdb=" CA LEU A 171 " pdb=" C LEU A 171 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.29e-02 6.01e+03 1.14e+01 bond pdb=" CG1 ILE C 266 " pdb=" CD1 ILE C 266 " ideal model delta sigma weight residual 1.513 1.383 0.130 3.90e-02 6.57e+02 1.11e+01 bond pdb=" CA ILE B 355 " pdb=" C ILE B 355 " ideal model delta sigma weight residual 1.524 1.481 0.042 1.30e-02 5.92e+03 1.06e+01 bond pdb=" CA ASP A 173 " pdb=" C ASP A 173 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.34e-02 5.57e+03 1.03e+01 bond pdb=" CA PRO B 409 " pdb=" C PRO B 409 " ideal model delta sigma weight residual 1.528 1.500 0.029 9.10e-03 1.21e+04 9.99e+00 ... (remaining 18652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 24321 2.53 - 5.05: 796 5.05 - 7.58: 123 7.58 - 10.10: 23 10.10 - 12.63: 8 Bond angle restraints: 25271 Sorted by residual: angle pdb=" N GLN B 161 " pdb=" CA GLN B 161 " pdb=" C GLN B 161 " ideal model delta sigma weight residual 109.39 122.02 -12.63 1.59e+00 3.96e-01 6.30e+01 angle pdb=" N SER B 419 " pdb=" CA SER B 419 " pdb=" C SER B 419 " ideal model delta sigma weight residual 109.52 97.25 12.27 1.55e+00 4.16e-01 6.27e+01 angle pdb=" N GLU B 162 " pdb=" CA GLU B 162 " pdb=" C GLU B 162 " ideal model delta sigma weight residual 109.72 97.12 12.60 1.60e+00 3.91e-01 6.20e+01 angle pdb=" N LEU B 100 " pdb=" CA LEU B 100 " pdb=" C LEU B 100 " ideal model delta sigma weight residual 112.59 103.05 9.54 1.22e+00 6.72e-01 6.11e+01 angle pdb=" N GLN B 420 " pdb=" CA GLN B 420 " pdb=" C GLN B 420 " ideal model delta sigma weight residual 112.24 104.09 8.15 1.28e+00 6.10e-01 4.05e+01 ... (remaining 25266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10045 17.97 - 35.94: 928 35.94 - 53.91: 120 53.91 - 71.89: 25 71.89 - 89.86: 13 Dihedral angle restraints: 11131 sinusoidal: 4267 harmonic: 6864 Sorted by residual: dihedral pdb=" C ASP B 353 " pdb=" N ASP B 353 " pdb=" CA ASP B 353 " pdb=" CB ASP B 353 " ideal model delta harmonic sigma weight residual -122.60 -137.73 15.13 0 2.50e+00 1.60e-01 3.66e+01 dihedral pdb=" N ASP B 353 " pdb=" C ASP B 353 " pdb=" CA ASP B 353 " pdb=" CB ASP B 353 " ideal model delta harmonic sigma weight residual 122.80 137.61 -14.81 0 2.50e+00 1.60e-01 3.51e+01 dihedral pdb=" CA PHE D 143 " pdb=" C PHE D 143 " pdb=" N GLY D 144 " pdb=" CA GLY D 144 " ideal model delta harmonic sigma weight residual -180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 11128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2649 0.132 - 0.263: 130 0.263 - 0.395: 11 0.395 - 0.526: 5 0.526 - 0.658: 3 Chirality restraints: 2798 Sorted by residual: chirality pdb=" CA ASP B 353 " pdb=" N ASP B 353 " pdb=" C ASP B 353 " pdb=" CB ASP B 353 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA ASP B 354 " pdb=" N ASP B 354 " pdb=" C ASP B 354 " pdb=" CB ASP B 354 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CA GLN B 161 " pdb=" N GLN B 161 " pdb=" C GLN B 161 " pdb=" CB GLN B 161 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.55 2.00e-01 2.50e+01 7.43e+00 ... (remaining 2795 not shown) Planarity restraints: 3348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 498 " 0.022 2.00e-02 2.50e+03 3.22e-02 2.07e+01 pdb=" CG TYR A 498 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR A 498 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 498 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 498 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 498 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 498 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 498 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 408 " -0.056 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 409 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 104 " -0.012 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR E 104 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR E 104 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 104 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR E 104 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 104 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 104 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 104 " 0.001 2.00e-02 2.50e+03 ... (remaining 3345 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 274 2.59 - 3.17: 15640 3.17 - 3.75: 31165 3.75 - 4.32: 43622 4.32 - 4.90: 71599 Nonbonded interactions: 162300 Sorted by model distance: nonbonded pdb=" O SER B 419 " pdb=" CD GLN B 420 " model vdw 2.014 3.270 nonbonded pdb=" O SER B 419 " pdb=" OE1 GLN B 420 " model vdw 2.068 3.040 nonbonded pdb=" C SER B 419 " pdb=" OE1 GLN B 420 " model vdw 2.172 3.270 nonbonded pdb=" OG SER E 103 " pdb=" NE2 GLN E 122 " model vdw 2.193 3.120 nonbonded pdb=" O SER C 326 " pdb=" OG SER C 358 " model vdw 2.212 3.040 ... (remaining 162295 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 92 through 158 or resid 167 through 569)) } ncs_group { reference = (chain 'C' and resid 2 through 432) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.360 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.010 0.130 18657 Z= 0.419 Angle : 1.103 12.625 25271 Z= 0.621 Chirality : 0.071 0.658 2798 Planarity : 0.007 0.086 3348 Dihedral : 13.995 89.856 6767 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.32 % Allowed : 1.06 % Favored : 98.62 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.15), residues: 2384 helix: -1.43 (0.13), residues: 1153 sheet: -1.50 (0.42), residues: 138 loop : -1.55 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 196 TYR 0.073 0.004 TYR A 498 PHE 0.051 0.004 PHE C 360 TRP 0.030 0.003 TRP A 447 HIS 0.016 0.002 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00950 (18657) covalent geometry : angle 1.10342 (25271) hydrogen bonds : bond 0.18285 ( 867) hydrogen bonds : angle 7.62765 ( 2499) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 210 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.8557 (pmm) cc_final: 0.8236 (pmm) REVERT: F 168 VAL cc_start: 0.8862 (t) cc_final: 0.8496 (m) outliers start: 6 outliers final: 1 residues processed: 216 average time/residue: 0.1316 time to fit residues: 42.4615 Evaluate side-chains 137 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 526 ASN ** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 ASN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.071867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.062000 restraints weight = 66906.021| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.61 r_work: 0.3133 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18657 Z= 0.132 Angle : 0.624 7.942 25271 Z= 0.332 Chirality : 0.043 0.163 2798 Planarity : 0.005 0.064 3348 Dihedral : 5.668 54.514 2628 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.95 % Allowed : 7.78 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.16), residues: 2384 helix: -0.09 (0.15), residues: 1155 sheet: -1.40 (0.41), residues: 134 loop : -1.31 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 111 TYR 0.024 0.002 TYR D 365 PHE 0.018 0.002 PHE C 360 TRP 0.018 0.002 TRP A 447 HIS 0.009 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00289 (18657) covalent geometry : angle 0.62428 (25271) hydrogen bonds : bond 0.04384 ( 867) hydrogen bonds : angle 5.43759 ( 2499) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8059 (tm-30) REVERT: A 284 ARG cc_start: 0.8851 (mmm160) cc_final: 0.8007 (ttt180) REVERT: A 468 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8047 (tp) REVERT: A 500 MET cc_start: 0.8336 (pmm) cc_final: 0.7312 (pmm) REVERT: A 558 MET cc_start: 0.8141 (tpp) cc_final: 0.7880 (tpp) REVERT: B 163 MET cc_start: 0.5280 (tmm) cc_final: 0.4892 (tmm) REVERT: C 125 MET cc_start: 0.8049 (mmm) cc_final: 0.7566 (mmm) REVERT: C 392 CYS cc_start: 0.8974 (m) cc_final: 0.8762 (p) REVERT: D 125 MET cc_start: 0.8872 (ppp) cc_final: 0.8657 (ptm) REVERT: E 28 LYS cc_start: 0.8364 (mtpp) cc_final: 0.8130 (mtpp) REVERT: F 60 MET cc_start: 0.7264 (ptp) cc_final: 0.5852 (mpp) REVERT: X 63 LYS cc_start: 0.7842 (tppt) cc_final: 0.7299 (tppt) outliers start: 18 outliers final: 8 residues processed: 172 average time/residue: 0.1097 time to fit residues: 30.4590 Evaluate side-chains 145 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain E residue 159 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS C 29 ASN ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN D 362 HIS ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 GLN F 220 ASN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.070712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.060565 restraints weight = 68385.162| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.59 r_work: 0.3094 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18657 Z= 0.130 Angle : 0.563 6.991 25271 Z= 0.298 Chirality : 0.042 0.160 2798 Planarity : 0.005 0.066 3348 Dihedral : 5.104 52.298 2628 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.43 % Allowed : 10.22 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.17), residues: 2384 helix: 0.48 (0.15), residues: 1183 sheet: -1.26 (0.42), residues: 134 loop : -1.12 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 111 TYR 0.023 0.001 TYR A 102 PHE 0.023 0.002 PHE E 105 TRP 0.017 0.001 TRP A 447 HIS 0.009 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00287 (18657) covalent geometry : angle 0.56331 (25271) hydrogen bonds : bond 0.03670 ( 867) hydrogen bonds : angle 4.97340 ( 2499) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.8482 (ttp) cc_final: 0.8245 (ttp) REVERT: A 128 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 558 MET cc_start: 0.8146 (tpp) cc_final: 0.7840 (tpp) REVERT: B 163 MET cc_start: 0.5302 (tmm) cc_final: 0.4654 (tmm) REVERT: C 125 MET cc_start: 0.7977 (mmm) cc_final: 0.7489 (mmm) REVERT: D 147 MET cc_start: 0.9219 (ptt) cc_final: 0.9016 (ptp) REVERT: E 28 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8173 (mtpp) REVERT: E 139 MET cc_start: 0.9130 (mmm) cc_final: 0.8887 (mmm) REVERT: X 63 LYS cc_start: 0.7889 (tppt) cc_final: 0.7297 (tppt) outliers start: 27 outliers final: 11 residues processed: 169 average time/residue: 0.1138 time to fit residues: 30.8260 Evaluate side-chains 144 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 230 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 214 optimal weight: 0.0670 chunk 60 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 194 optimal weight: 0.0370 chunk 232 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 494 ASN D 29 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.070148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.059980 restraints weight = 68542.169| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.58 r_work: 0.3084 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18657 Z= 0.129 Angle : 0.551 7.089 25271 Z= 0.290 Chirality : 0.042 0.157 2798 Planarity : 0.004 0.064 3348 Dihedral : 4.916 51.020 2628 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.59 % Allowed : 11.91 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.17), residues: 2384 helix: 0.73 (0.16), residues: 1192 sheet: -1.14 (0.43), residues: 134 loop : -1.01 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 284 TYR 0.025 0.001 TYR A 102 PHE 0.019 0.001 PHE E 105 TRP 0.015 0.001 TRP A 447 HIS 0.009 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00289 (18657) covalent geometry : angle 0.55089 (25271) hydrogen bonds : bond 0.03458 ( 867) hydrogen bonds : angle 4.87282 ( 2499) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 284 ARG cc_start: 0.8913 (mmm160) cc_final: 0.8692 (mmm160) REVERT: A 558 MET cc_start: 0.8208 (tpp) cc_final: 0.7764 (tpp) REVERT: B 163 MET cc_start: 0.5088 (tmm) cc_final: 0.4730 (tmm) REVERT: D 22 MET cc_start: 0.9048 (mmp) cc_final: 0.8676 (mmm) REVERT: E 28 LYS cc_start: 0.8418 (mtpp) cc_final: 0.8169 (mtpp) REVERT: F 60 MET cc_start: 0.7445 (ptp) cc_final: 0.6054 (mpp) REVERT: X 28 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: X 63 LYS cc_start: 0.7887 (tppt) cc_final: 0.7278 (tppt) REVERT: X 81 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7458 (mp) outliers start: 30 outliers final: 13 residues processed: 170 average time/residue: 0.1250 time to fit residues: 33.5950 Evaluate side-chains 146 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain X residue 28 GLN Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 89 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN B 494 ASN C 182 ASN C 315 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.069716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059655 restraints weight = 68723.689| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.56 r_work: 0.3060 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18657 Z= 0.133 Angle : 0.544 7.046 25271 Z= 0.285 Chirality : 0.042 0.263 2798 Planarity : 0.004 0.063 3348 Dihedral : 4.812 49.312 2628 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.32 % Allowed : 12.81 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.17), residues: 2384 helix: 0.87 (0.16), residues: 1191 sheet: -1.14 (0.44), residues: 132 loop : -0.96 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 424 TYR 0.025 0.001 TYR A 102 PHE 0.015 0.001 PHE E 101 TRP 0.015 0.001 TRP A 447 HIS 0.009 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00303 (18657) covalent geometry : angle 0.54389 (25271) hydrogen bonds : bond 0.03464 ( 867) hydrogen bonds : angle 4.79735 ( 2499) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8440 (ttp) cc_final: 0.8142 (ttp) REVERT: A 128 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8443 (tm-30) REVERT: A 558 MET cc_start: 0.8113 (tpp) cc_final: 0.7680 (tpp) REVERT: B 108 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7820 (mmm) REVERT: B 163 MET cc_start: 0.5137 (tmm) cc_final: 0.4682 (tmm) REVERT: C 142 MET cc_start: 0.8148 (ppp) cc_final: 0.7809 (tmm) REVERT: D 22 MET cc_start: 0.9097 (mmp) cc_final: 0.8698 (mmm) REVERT: E 28 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8175 (mtpp) REVERT: X 28 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: X 29 LYS cc_start: 0.9220 (mtmm) cc_final: 0.8777 (mtmm) REVERT: X 63 LYS cc_start: 0.7955 (tppt) cc_final: 0.7301 (tppt) REVERT: X 81 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7478 (mp) outliers start: 25 outliers final: 14 residues processed: 154 average time/residue: 0.1294 time to fit residues: 32.2704 Evaluate side-chains 147 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain X residue 28 GLN Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 100 optimal weight: 0.0270 chunk 152 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 chunk 174 optimal weight: 0.2980 chunk 112 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 214 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN B 494 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.071666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.061607 restraints weight = 67513.317| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.57 r_work: 0.3129 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18657 Z= 0.098 Angle : 0.520 7.457 25271 Z= 0.270 Chirality : 0.041 0.163 2798 Planarity : 0.004 0.064 3348 Dihedral : 4.658 48.277 2628 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.38 % Allowed : 14.24 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.18), residues: 2384 helix: 1.00 (0.16), residues: 1188 sheet: -1.09 (0.42), residues: 139 loop : -0.87 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 284 TYR 0.025 0.001 TYR A 102 PHE 0.017 0.001 PHE E 105 TRP 0.018 0.001 TRP A 447 HIS 0.009 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00217 (18657) covalent geometry : angle 0.51951 (25271) hydrogen bonds : bond 0.03101 ( 867) hydrogen bonds : angle 4.71426 ( 2499) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8532 (tm-30) REVERT: A 284 ARG cc_start: 0.8927 (mmm160) cc_final: 0.8677 (mmm160) REVERT: A 558 MET cc_start: 0.8096 (tpp) cc_final: 0.7655 (tpp) REVERT: B 163 MET cc_start: 0.5425 (tmm) cc_final: 0.4897 (tmm) REVERT: C 142 MET cc_start: 0.8066 (ppp) cc_final: 0.7803 (tmm) REVERT: C 168 MET cc_start: 0.8914 (ptp) cc_final: 0.8562 (ptp) REVERT: D 22 MET cc_start: 0.9096 (mmp) cc_final: 0.8704 (mmm) REVERT: D 125 MET cc_start: 0.8399 (ptm) cc_final: 0.8172 (ptp) REVERT: E 28 LYS cc_start: 0.8367 (mtpp) cc_final: 0.8110 (mtpp) REVERT: X 28 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: X 81 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7442 (mp) outliers start: 26 outliers final: 14 residues processed: 178 average time/residue: 0.1304 time to fit residues: 37.4243 Evaluate side-chains 152 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain X residue 28 GLN Chi-restraints excluded: chain X residue 81 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 41 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 90 optimal weight: 0.0770 chunk 113 optimal weight: 0.4980 chunk 151 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 203 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 494 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN ** X 46 GLN ** 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 = 0.3500 r_free = 0.3500 target = 0.071519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.061443 restraints weight = 68199.429| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.58 r_work: 0.3126 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18657 Z= 0.103 Angle : 0.531 9.161 25271 Z= 0.273 Chirality : 0.041 0.157 2798 Planarity : 0.004 0.064 3348 Dihedral : 4.548 47.603 2628 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.18 % Rotamer: Outliers : 1.59 % Allowed : 14.72 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.18), residues: 2384 helix: 1.15 (0.16), residues: 1181 sheet: -0.99 (0.44), residues: 132 loop : -0.82 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 284 TYR 0.012 0.001 TYR D 365 PHE 0.012 0.001 PHE E 101 TRP 0.016 0.001 TRP A 447 HIS 0.009 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00233 (18657) covalent geometry : angle 0.53056 (25271) hydrogen bonds : bond 0.03148 ( 867) hydrogen bonds : angle 4.68023 ( 2499) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 MET cc_start: 0.8104 (tpp) cc_final: 0.7667 (tpp) REVERT: B 163 MET cc_start: 0.5378 (tmm) cc_final: 0.4825 (tmm) REVERT: B 255 MET cc_start: 0.8432 (mpp) cc_final: 0.7768 (mtm) REVERT: C 168 MET cc_start: 0.8959 (ptp) cc_final: 0.8631 (ptp) REVERT: D 22 MET cc_start: 0.9090 (mmp) cc_final: 0.8684 (mmm) REVERT: D 73 TYR cc_start: 0.7096 (t80) cc_final: 0.6433 (t80) REVERT: E 28 LYS cc_start: 0.8368 (mtpp) cc_final: 0.8112 (mtpp) REVERT: F 131 MET cc_start: 0.7659 (tmm) cc_final: 0.7396 (ttp) REVERT: X 28 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: X 29 LYS cc_start: 0.9178 (mtmm) cc_final: 0.8737 (mtmm) REVERT: X 63 LYS cc_start: 0.8052 (tppt) cc_final: 0.7396 (tppt) REVERT: X 81 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7446 (mp) outliers start: 30 outliers final: 19 residues processed: 169 average time/residue: 0.1243 time to fit residues: 34.1259 Evaluate side-chains 156 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain X residue 28 GLN Chi-restraints excluded: chain X residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 494 ASN D 29 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 46 GLN ** 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 = 0.3463 r_free = 0.3463 target = 0.070049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059951 restraints weight = 68375.028| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.55 r_work: 0.3084 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18657 Z= 0.143 Angle : 0.559 9.599 25271 Z= 0.291 Chirality : 0.042 0.164 2798 Planarity : 0.004 0.062 3348 Dihedral : 4.566 47.085 2628 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 1.48 % Allowed : 15.40 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.18), residues: 2384 helix: 1.18 (0.16), residues: 1181 sheet: -1.05 (0.44), residues: 132 loop : -0.75 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 284 TYR 0.019 0.001 TYR A 102 PHE 0.029 0.002 PHE A 549 TRP 0.015 0.001 TRP A 447 HIS 0.008 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00325 (18657) covalent geometry : angle 0.55935 (25271) hydrogen bonds : bond 0.03394 ( 867) hydrogen bonds : angle 4.70284 ( 2499) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 HIS cc_start: 0.8243 (t-90) cc_final: 0.7875 (t-90) REVERT: A 284 ARG cc_start: 0.8931 (mmm160) cc_final: 0.8010 (ttt180) REVERT: A 558 MET cc_start: 0.8159 (tpp) cc_final: 0.7698 (tpp) REVERT: B 163 MET cc_start: 0.5322 (tmm) cc_final: 0.4734 (tmm) REVERT: B 255 MET cc_start: 0.8522 (mpp) cc_final: 0.7634 (mtm) REVERT: C 168 MET cc_start: 0.8993 (ptp) cc_final: 0.8776 (ptp) REVERT: D 22 MET cc_start: 0.9108 (mmp) cc_final: 0.8807 (mmm) REVERT: D 404 PHE cc_start: 0.7685 (m-80) cc_final: 0.7089 (m-80) REVERT: E 28 LYS cc_start: 0.8426 (mtpp) cc_final: 0.8177 (mtpp) REVERT: F 131 MET cc_start: 0.7731 (tmm) cc_final: 0.7433 (ttp) REVERT: X 28 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: X 63 LYS cc_start: 0.8030 (tppt) cc_final: 0.7700 (tppt) outliers start: 28 outliers final: 17 residues processed: 161 average time/residue: 0.1119 time to fit residues: 29.1775 Evaluate side-chains 149 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain X residue 28 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 230 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 233 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 207 optimal weight: 0.4980 chunk 178 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 494 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN ** X 46 GLN ** 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 = 0.3467 r_free = 0.3467 target = 0.070096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059951 restraints weight = 68254.070| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.57 r_work: 0.3090 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18657 Z= 0.129 Angle : 0.556 8.354 25271 Z= 0.288 Chirality : 0.042 0.216 2798 Planarity : 0.004 0.062 3348 Dihedral : 4.571 47.068 2628 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 1.59 % Allowed : 15.46 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.18), residues: 2384 helix: 1.14 (0.16), residues: 1185 sheet: -1.04 (0.44), residues: 134 loop : -0.71 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 284 TYR 0.013 0.001 TYR D 365 PHE 0.023 0.001 PHE A 549 TRP 0.016 0.001 TRP A 447 HIS 0.008 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00294 (18657) covalent geometry : angle 0.55649 (25271) hydrogen bonds : bond 0.03309 ( 867) hydrogen bonds : angle 4.70581 ( 2499) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 HIS cc_start: 0.8226 (t-90) cc_final: 0.7852 (t-90) REVERT: A 284 ARG cc_start: 0.8856 (mmm160) cc_final: 0.8639 (mmm160) REVERT: A 558 MET cc_start: 0.8185 (tpp) cc_final: 0.7700 (tpp) REVERT: B 163 MET cc_start: 0.5304 (tmm) cc_final: 0.4710 (tmm) REVERT: B 255 MET cc_start: 0.8509 (mpp) cc_final: 0.7574 (mtm) REVERT: B 327 LEU cc_start: 0.9330 (tt) cc_final: 0.9077 (tt) REVERT: C 168 MET cc_start: 0.8992 (ptp) cc_final: 0.8776 (ptp) REVERT: D 22 MET cc_start: 0.9133 (mmp) cc_final: 0.8714 (mmm) REVERT: D 404 PHE cc_start: 0.7727 (m-80) cc_final: 0.7099 (m-80) REVERT: E 28 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8159 (mtpp) REVERT: X 28 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: X 44 MET cc_start: 0.7403 (tpt) cc_final: 0.6901 (tpp) REVERT: X 63 LYS cc_start: 0.8055 (tppt) cc_final: 0.7713 (tppt) outliers start: 30 outliers final: 23 residues processed: 159 average time/residue: 0.1018 time to fit residues: 26.5607 Evaluate side-chains 155 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 134 CYS Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain X residue 28 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 494 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN ** X 46 GLN ** 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 = 0.3472 r_free = 0.3472 target = 0.070651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.060537 restraints weight = 67807.689| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.56 r_work: 0.3094 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18657 Z= 0.121 Angle : 0.567 14.929 25271 Z= 0.288 Chirality : 0.042 0.158 2798 Planarity : 0.004 0.062 3348 Dihedral : 4.548 47.026 2628 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 1.38 % Allowed : 15.62 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.18), residues: 2384 helix: 1.18 (0.16), residues: 1182 sheet: -0.96 (0.44), residues: 134 loop : -0.68 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 284 TYR 0.012 0.001 TYR D 365 PHE 0.022 0.001 PHE E 105 TRP 0.016 0.001 TRP A 447 HIS 0.008 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00275 (18657) covalent geometry : angle 0.56657 (25271) hydrogen bonds : bond 0.03250 ( 867) hydrogen bonds : angle 4.66606 ( 2499) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 HIS cc_start: 0.8224 (t-90) cc_final: 0.7849 (t-90) REVERT: A 284 ARG cc_start: 0.8853 (mmm160) cc_final: 0.8634 (mmm160) REVERT: A 558 MET cc_start: 0.8185 (tpp) cc_final: 0.7704 (tpp) REVERT: B 163 MET cc_start: 0.5285 (tmm) cc_final: 0.4687 (tmm) REVERT: B 255 MET cc_start: 0.8482 (mpp) cc_final: 0.7520 (mtm) REVERT: C 168 MET cc_start: 0.9000 (ptp) cc_final: 0.8785 (ptp) REVERT: D 22 MET cc_start: 0.9140 (mmp) cc_final: 0.8718 (mmm) REVERT: D 404 PHE cc_start: 0.7733 (m-80) cc_final: 0.7101 (m-80) REVERT: E 28 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8196 (mtpp) REVERT: X 28 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7776 (pm20) REVERT: X 44 MET cc_start: 0.7378 (tpt) cc_final: 0.6881 (tpp) REVERT: X 63 LYS cc_start: 0.8058 (tppt) cc_final: 0.7433 (tppt) outliers start: 26 outliers final: 19 residues processed: 156 average time/residue: 0.1091 time to fit residues: 27.7504 Evaluate side-chains 152 residues out of total 1889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 134 CYS Chi-restraints excluded: chain X residue 28 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 85 optimal weight: 0.0570 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.069301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.059142 restraints weight = 68669.082| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.56 r_work: 0.3065 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18657 Z= 0.145 Angle : 0.578 16.539 25271 Z= 0.295 Chirality : 0.042 0.159 2798 Planarity : 0.004 0.061 3348 Dihedral : 4.563 46.391 2628 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.02 % Rotamer: Outliers : 1.32 % Allowed : 15.72 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.18), residues: 2384 helix: 1.14 (0.16), residues: 1187 sheet: -0.94 (0.45), residues: 132 loop : -0.65 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 284 TYR 0.013 0.001 TYR C 331 PHE 0.020 0.002 PHE A 549 TRP 0.016 0.001 TRP A 447 HIS 0.008 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00333 (18657) covalent geometry : angle 0.57843 (25271) hydrogen bonds : bond 0.03405 ( 867) hydrogen bonds : angle 4.66777 ( 2499) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2836.91 seconds wall clock time: 50 minutes 9.14 seconds (3009.14 seconds total)