Starting phenix.real_space_refine on Sun Apr 5 02:33:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mcv_63807/04_2026/9mcv_63807_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mcv_63807/04_2026/9mcv_63807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mcv_63807/04_2026/9mcv_63807_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mcv_63807/04_2026/9mcv_63807_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mcv_63807/04_2026/9mcv_63807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mcv_63807/04_2026/9mcv_63807.map" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.110 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 30 5.16 5 C 4808 2.51 5 N 1108 2.21 5 O 1258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7204 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3557 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 450} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'LMR': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B Time building chain proxies: 2.48, per 1000 atoms: 0.34 Number of scatterers: 7204 At special positions: 0 Unit cell: (86.676, 103.452, 76.424, 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 30 16.00 O 1258 8.00 N 1108 7.00 C 4808 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: 0.65 Conformation dependent library (CDL) restraints added in 283.3 milliseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 78.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 95 through 112 removed outlier: 3.621A pdb=" N SER A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 140 removed outlier: 3.847A pdb=" N SER A 128 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.551A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 168 through 171 removed outlier: 3.735A pdb=" N THR A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 172 through 191 removed outlier: 3.642A pdb=" N TRP A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 removed outlier: 3.581A pdb=" N THR A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.552A pdb=" N THR A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.660A pdb=" N ARG A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.883A pdb=" N SER A 244 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.768A pdb=" N LEU A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.610A pdb=" N ALA A 283 " --> pdb=" O PHE A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 284 through 291 removed outlier: 4.199A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 321 removed outlier: 3.715A pdb=" N PHE A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix removed outlier: 3.877A pdb=" N SER A 319 " --> pdb=" O PRO A 315 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.734A pdb=" N LYS A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 removed outlier: 3.557A pdb=" N THR A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 375 through 380 removed outlier: 4.084A pdb=" N LEU A 379 " --> pdb=" O CYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 397 removed outlier: 3.672A pdb=" N ALA A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 407 removed outlier: 3.752A pdb=" N CYS A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 431 removed outlier: 3.821A pdb=" N TRP A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 416 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 440 removed outlier: 3.770A pdb=" N TRP A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 466 removed outlier: 4.529A pdb=" N GLY A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLN A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 490 removed outlier: 3.863A pdb=" N HIS A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N SER A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.599A pdb=" N ALA A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.571A pdb=" N ALA A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 552 removed outlier: 3.802A pdb=" N ILE A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 539 " --> pdb=" O PHE A 535 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 542 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 548 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 561 removed outlier: 3.719A pdb=" N TRP A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS A 558 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 removed outlier: 3.621A pdb=" N SER B 102 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 108 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 140 removed outlier: 3.847A pdb=" N SER B 128 " --> pdb=" O TRP B 124 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 138 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.551A pdb=" N ILE B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 168 through 171 removed outlier: 3.734A pdb=" N THR B 171 " --> pdb=" O SER B 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 168 through 171' Processing helix chain 'B' and resid 172 through 191 removed outlier: 3.643A pdb=" N TRP B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 186 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 187 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 205 removed outlier: 3.581A pdb=" N THR B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 200 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 213 through 218 removed outlier: 3.552A pdb=" N THR B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.660A pdb=" N ARG B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.882A pdb=" N SER B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.768A pdb=" N LEU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.609A pdb=" N ALA B 283 " --> pdb=" O PHE B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 284 through 291 removed outlier: 4.199A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 321 removed outlier: 3.715A pdb=" N PHE B 309 " --> pdb=" O TRP B 305 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 310 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Proline residue: B 315 - end of helix removed outlier: 3.877A pdb=" N SER B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 331 removed outlier: 3.733A pdb=" N LYS B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 removed outlier: 3.558A pdb=" N THR B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 375 Processing helix chain 'B' and resid 375 through 380 removed outlier: 4.083A pdb=" N LEU B 379 " --> pdb=" O CYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 397 removed outlier: 3.672A pdb=" N ALA B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 407 removed outlier: 3.753A pdb=" N CYS B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 431 removed outlier: 3.820A pdb=" N TRP B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 414 " --> pdb=" O SER B 410 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 416 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 428 " --> pdb=" O MET B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 removed outlier: 3.769A pdb=" N TRP B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS B 440 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 466 removed outlier: 4.529A pdb=" N GLY B 457 " --> pdb=" O PRO B 453 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLN B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 490 removed outlier: 3.863A pdb=" N HIS B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 477 " --> pdb=" O GLN B 473 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N SER B 482 " --> pdb=" O GLY B 478 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 508 removed outlier: 3.600A pdb=" N ALA B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 525 removed outlier: 3.571A pdb=" N ALA B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 552 removed outlier: 3.803A pdb=" N ILE B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 539 " --> pdb=" O PHE B 535 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 542 " --> pdb=" O GLY B 538 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 561 removed outlier: 3.719A pdb=" N TRP B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS B 558 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 990 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: 0.78 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1084 1.27 - 1.40: 1872 1.40 - 1.54: 4363 1.54 - 1.67: 35 1.67 - 1.81: 48 Bond restraints: 7402 Sorted by residual: bond pdb=" N PHE B 509 " pdb=" CA PHE B 509 " ideal model delta sigma weight residual 1.457 1.363 0.094 1.29e-02 6.01e+03 5.28e+01 bond pdb=" N PHE A 509 " pdb=" CA PHE A 509 " ideal model delta sigma weight residual 1.457 1.363 0.094 1.29e-02 6.01e+03 5.28e+01 bond pdb=" C ALA B 283 " pdb=" O ALA B 283 " ideal model delta sigma weight residual 1.235 1.141 0.094 1.38e-02 5.25e+03 4.62e+01 bond pdb=" C ALA A 283 " pdb=" O ALA A 283 " ideal model delta sigma weight residual 1.235 1.141 0.093 1.38e-02 5.25e+03 4.59e+01 bond pdb=" C THR B 282 " pdb=" O THR B 282 " ideal model delta sigma weight residual 1.236 1.146 0.090 1.34e-02 5.57e+03 4.52e+01 ... (remaining 7397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 9792 2.87 - 5.74: 279 5.74 - 8.60: 47 8.60 - 11.47: 12 11.47 - 14.34: 2 Bond angle restraints: 10132 Sorted by residual: angle pdb=" N GLU A 117 " pdb=" CA GLU A 117 " pdb=" C GLU A 117 " ideal model delta sigma weight residual 110.30 124.64 -14.34 1.50e+00 4.44e-01 9.14e+01 angle pdb=" N GLU B 117 " pdb=" CA GLU B 117 " pdb=" C GLU B 117 " ideal model delta sigma weight residual 110.30 124.62 -14.32 1.50e+00 4.44e-01 9.11e+01 angle pdb=" C PRO A 116 " pdb=" CA PRO A 116 " pdb=" CB PRO A 116 " ideal model delta sigma weight residual 111.23 102.74 8.49 1.28e+00 6.10e-01 4.40e+01 angle pdb=" C PRO B 116 " pdb=" CA PRO B 116 " pdb=" CB PRO B 116 " ideal model delta sigma weight residual 111.23 102.75 8.48 1.28e+00 6.10e-01 4.39e+01 angle pdb=" N LYS B 443 " pdb=" CA LYS B 443 " pdb=" C LYS B 443 " ideal model delta sigma weight residual 114.62 107.17 7.45 1.14e+00 7.69e-01 4.27e+01 ... (remaining 10127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 3844 15.00 - 30.01: 398 30.01 - 45.01: 78 45.01 - 60.02: 18 60.02 - 75.02: 2 Dihedral angle restraints: 4340 sinusoidal: 1646 harmonic: 2694 Sorted by residual: dihedral pdb=" CA HIS B 467 " pdb=" C HIS B 467 " pdb=" N TYR B 468 " pdb=" CA TYR B 468 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA HIS A 467 " pdb=" C HIS A 467 " pdb=" N TYR A 468 " pdb=" CA TYR A 468 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" C PRO A 116 " pdb=" N PRO A 116 " pdb=" CA PRO A 116 " pdb=" CB PRO A 116 " ideal model delta harmonic sigma weight residual -120.70 -109.65 -11.05 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 4337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 984 0.068 - 0.135: 196 0.135 - 0.203: 24 0.203 - 0.271: 10 0.271 - 0.339: 2 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CA PHE B 509 " pdb=" N PHE B 509 " pdb=" C PHE B 509 " pdb=" CB PHE B 509 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA PHE A 509 " pdb=" N PHE A 509 " pdb=" C PHE A 509 " pdb=" CB PHE A 509 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA TRP A 556 " pdb=" N TRP A 556 " pdb=" C TRP A 556 " pdb=" CB TRP A 556 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1213 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 560 " 0.027 2.00e-02 2.50e+03 5.39e-02 2.90e+01 pdb=" C LEU B 560 " -0.093 2.00e-02 2.50e+03 pdb=" O LEU B 560 " 0.035 2.00e-02 2.50e+03 pdb=" N GLY B 561 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 560 " -0.027 2.00e-02 2.50e+03 5.39e-02 2.90e+01 pdb=" C LEU A 560 " 0.093 2.00e-02 2.50e+03 pdb=" O LEU A 560 " -0.035 2.00e-02 2.50e+03 pdb=" N GLY A 561 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 508 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C LEU A 508 " 0.068 2.00e-02 2.50e+03 pdb=" O LEU A 508 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE A 509 " -0.024 2.00e-02 2.50e+03 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 60 2.60 - 3.18: 5693 3.18 - 3.75: 9955 3.75 - 4.33: 15843 4.33 - 4.90: 25249 Nonbonded interactions: 56800 Sorted by model distance: nonbonded pdb=" O GLY B 250 " pdb=" OG SER B 257 " model vdw 2.027 3.040 nonbonded pdb=" O GLY A 250 " pdb=" OG SER A 257 " model vdw 2.027 3.040 nonbonded pdb=" OE1 GLN A 125 " pdb=" OG1 THR A 160 " model vdw 2.034 3.040 nonbonded pdb=" OE1 GLN B 125 " pdb=" OG1 THR B 160 " model vdw 2.035 3.040 nonbonded pdb=" O ASN B 505 " pdb=" CD2 PHE B 509 " model vdw 2.087 3.340 ... (remaining 56795 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.012 0.098 7402 Z= 0.649 Angle : 1.151 14.338 10132 Z= 0.666 Chirality : 0.061 0.339 1216 Planarity : 0.008 0.058 1212 Dihedral : 12.868 75.022 2616 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.53 % Allowed : 4.81 % Favored : 94.65 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.59 (0.16), residues: 942 helix: -4.54 (0.09), residues: 724 sheet: None (None), residues: 0 loop : -2.49 (0.35), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 233 TYR 0.032 0.003 TYR B 563 PHE 0.035 0.004 PHE B 509 TRP 0.023 0.003 TRP A 556 HIS 0.006 0.003 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.01172 ( 7402) covalent geometry : angle 1.15122 (10132) hydrogen bonds : bond 0.39655 ( 330) hydrogen bonds : angle 10.77614 ( 990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.258 Fit side-chains REVERT: A 207 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7920 (ttpp) REVERT: A 388 MET cc_start: 0.9136 (mtp) cc_final: 0.8931 (mtm) REVERT: B 388 MET cc_start: 0.9142 (mtp) cc_final: 0.8915 (mtm) outliers start: 4 outliers final: 1 residues processed: 115 average time/residue: 0.4705 time to fit residues: 57.7193 Evaluate side-chains 63 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 401 ASN A 505 ASN B 92 GLN B 401 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.108903 restraints weight = 9136.676| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.59 r_work: 0.3060 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7402 Z= 0.143 Angle : 0.642 5.804 10132 Z= 0.330 Chirality : 0.041 0.135 1216 Planarity : 0.006 0.042 1212 Dihedral : 7.340 48.613 1140 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.20 % Allowed : 9.89 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.22), residues: 942 helix: -2.77 (0.15), residues: 732 sheet: None (None), residues: 0 loop : -2.00 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 233 TYR 0.009 0.001 TYR B 331 PHE 0.018 0.001 PHE A 559 TRP 0.019 0.001 TRP B 417 HIS 0.003 0.001 HIS B 467 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7402) covalent geometry : angle 0.64161 (10132) hydrogen bonds : bond 0.06099 ( 330) hydrogen bonds : angle 4.87886 ( 990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.257 Fit side-chains REVERT: A 131 LEU cc_start: 0.7771 (tp) cc_final: 0.7163 (mm) REVERT: A 388 MET cc_start: 0.9051 (mtp) cc_final: 0.8814 (mtm) REVERT: A 437 MET cc_start: 0.8036 (mtm) cc_final: 0.7816 (mtm) REVERT: B 131 LEU cc_start: 0.7643 (tp) cc_final: 0.7051 (mm) REVERT: B 388 MET cc_start: 0.9068 (mtp) cc_final: 0.8852 (mtm) outliers start: 9 outliers final: 2 residues processed: 87 average time/residue: 0.4244 time to fit residues: 39.7452 Evaluate side-chains 62 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain B residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 65 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.0870 chunk 69 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 460 GLN B 505 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.115411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.093180 restraints weight = 8703.013| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.56 r_work: 0.2949 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7402 Z= 0.130 Angle : 0.603 6.104 10132 Z= 0.304 Chirality : 0.040 0.123 1216 Planarity : 0.005 0.043 1212 Dihedral : 6.761 52.023 1138 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.60 % Allowed : 11.36 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.25), residues: 942 helix: -1.65 (0.17), residues: 730 sheet: None (None), residues: 0 loop : -1.69 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 196 TYR 0.008 0.001 TYR A 463 PHE 0.021 0.001 PHE A 559 TRP 0.017 0.001 TRP B 452 HIS 0.004 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7402) covalent geometry : angle 0.60310 (10132) hydrogen bonds : bond 0.05563 ( 330) hydrogen bonds : angle 4.35698 ( 990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.261 Fit side-chains REVERT: A 104 SER cc_start: 0.8650 (t) cc_final: 0.7966 (p) REVERT: A 115 VAL cc_start: 0.8001 (p) cc_final: 0.7770 (t) REVERT: A 131 LEU cc_start: 0.7963 (tp) cc_final: 0.7282 (mm) REVERT: A 330 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7244 (mp) REVERT: B 104 SER cc_start: 0.8685 (t) cc_final: 0.7980 (p) REVERT: B 115 VAL cc_start: 0.8002 (p) cc_final: 0.7790 (t) REVERT: B 131 LEU cc_start: 0.7943 (tp) cc_final: 0.7275 (mm) REVERT: B 330 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7259 (mp) outliers start: 12 outliers final: 4 residues processed: 69 average time/residue: 0.3763 time to fit residues: 28.3379 Evaluate side-chains 60 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 460 GLN B 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.115184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.094194 restraints weight = 9148.679| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.48 r_work: 0.2851 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7402 Z= 0.134 Angle : 0.598 6.647 10132 Z= 0.301 Chirality : 0.041 0.122 1216 Planarity : 0.005 0.044 1212 Dihedral : 6.610 59.614 1138 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.27 % Allowed : 10.83 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.26), residues: 942 helix: -0.92 (0.18), residues: 742 sheet: None (None), residues: 0 loop : -1.46 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 196 TYR 0.010 0.001 TYR A 331 PHE 0.015 0.002 PHE B 509 TRP 0.018 0.001 TRP A 452 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7402) covalent geometry : angle 0.59842 (10132) hydrogen bonds : bond 0.05404 ( 330) hydrogen bonds : angle 4.24789 ( 990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.271 Fit side-chains REVERT: A 104 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.7940 (p) REVERT: A 131 LEU cc_start: 0.7740 (tp) cc_final: 0.7281 (tp) REVERT: A 330 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7291 (mp) REVERT: B 104 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.7941 (p) REVERT: B 131 LEU cc_start: 0.7773 (tp) cc_final: 0.7325 (tp) REVERT: B 330 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7252 (mp) REVERT: B 350 LYS cc_start: 0.8028 (mmmm) cc_final: 0.7651 (mtpp) outliers start: 17 outliers final: 10 residues processed: 71 average time/residue: 0.4076 time to fit residues: 31.3133 Evaluate side-chains 72 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 71 optimal weight: 0.0980 chunk 24 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.092711 restraints weight = 8709.300| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.57 r_work: 0.2875 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7402 Z= 0.098 Angle : 0.531 6.604 10132 Z= 0.266 Chirality : 0.039 0.117 1216 Planarity : 0.004 0.041 1212 Dihedral : 6.180 54.640 1138 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.41 % Allowed : 12.57 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.27), residues: 942 helix: -0.16 (0.19), residues: 734 sheet: None (None), residues: 0 loop : -1.49 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 196 TYR 0.007 0.001 TYR A 331 PHE 0.014 0.001 PHE B 509 TRP 0.013 0.001 TRP A 452 HIS 0.002 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 7402) covalent geometry : angle 0.53128 (10132) hydrogen bonds : bond 0.03950 ( 330) hydrogen bonds : angle 4.06138 ( 990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.284 Fit side-chains REVERT: A 104 SER cc_start: 0.8641 (t) cc_final: 0.7959 (p) REVERT: A 115 VAL cc_start: 0.8006 (p) cc_final: 0.7779 (t) REVERT: A 131 LEU cc_start: 0.7914 (tp) cc_final: 0.7450 (tp) REVERT: A 330 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7298 (mp) REVERT: B 104 SER cc_start: 0.8647 (t) cc_final: 0.7969 (p) REVERT: B 115 VAL cc_start: 0.7991 (p) cc_final: 0.7784 (t) REVERT: B 131 LEU cc_start: 0.7892 (tp) cc_final: 0.7429 (tp) REVERT: B 330 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7284 (mp) REVERT: B 350 LYS cc_start: 0.8065 (mmmm) cc_final: 0.7783 (mtpp) outliers start: 18 outliers final: 8 residues processed: 69 average time/residue: 0.3316 time to fit residues: 25.1325 Evaluate side-chains 65 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.090796 restraints weight = 9175.560| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.47 r_work: 0.2802 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7402 Z= 0.189 Angle : 0.667 6.785 10132 Z= 0.335 Chirality : 0.044 0.135 1216 Planarity : 0.005 0.046 1212 Dihedral : 6.667 51.321 1138 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.81 % Allowed : 12.57 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.27), residues: 942 helix: -0.34 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -1.38 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 233 TYR 0.011 0.002 TYR A 331 PHE 0.017 0.002 PHE B 238 TRP 0.012 0.002 TRP B 308 HIS 0.005 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 7402) covalent geometry : angle 0.66719 (10132) hydrogen bonds : bond 0.06663 ( 330) hydrogen bonds : angle 4.37420 ( 990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.256 Fit side-chains REVERT: A 104 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.7888 (p) REVERT: A 131 LEU cc_start: 0.7808 (tp) cc_final: 0.7359 (tp) REVERT: A 330 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7374 (mp) REVERT: B 104 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.7885 (p) REVERT: B 131 LEU cc_start: 0.7803 (tp) cc_final: 0.7357 (tp) REVERT: B 330 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7378 (mp) REVERT: B 350 LYS cc_start: 0.8024 (mmmm) cc_final: 0.7729 (mtpp) outliers start: 21 outliers final: 9 residues processed: 69 average time/residue: 0.4622 time to fit residues: 34.2445 Evaluate side-chains 72 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 87 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.091513 restraints weight = 8822.522| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.58 r_work: 0.2853 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7402 Z= 0.102 Angle : 0.535 6.753 10132 Z= 0.268 Chirality : 0.039 0.118 1216 Planarity : 0.004 0.040 1212 Dihedral : 6.122 47.591 1138 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.27 % Allowed : 12.97 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.28), residues: 942 helix: 0.31 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -1.47 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 259 TYR 0.007 0.001 TYR A 331 PHE 0.015 0.001 PHE B 509 TRP 0.015 0.001 TRP A 452 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 7402) covalent geometry : angle 0.53489 (10132) hydrogen bonds : bond 0.04014 ( 330) hydrogen bonds : angle 4.08274 ( 990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.276 Fit side-chains REVERT: A 104 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.7878 (p) REVERT: A 131 LEU cc_start: 0.7934 (tp) cc_final: 0.7440 (tp) REVERT: A 330 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7305 (mp) REVERT: B 104 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.7877 (p) REVERT: B 131 LEU cc_start: 0.7907 (tp) cc_final: 0.7433 (tp) REVERT: B 330 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7289 (mp) REVERT: B 350 LYS cc_start: 0.8059 (mmmm) cc_final: 0.7830 (mtpp) outliers start: 17 outliers final: 10 residues processed: 64 average time/residue: 0.3604 time to fit residues: 25.3094 Evaluate side-chains 68 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 58 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.114522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.092131 restraints weight = 8728.727| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.58 r_work: 0.2858 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7402 Z= 0.101 Angle : 0.533 7.033 10132 Z= 0.266 Chirality : 0.039 0.118 1216 Planarity : 0.004 0.040 1212 Dihedral : 5.909 43.311 1138 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.87 % Allowed : 14.04 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.28), residues: 942 helix: 0.58 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -1.38 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 259 TYR 0.006 0.001 TYR A 331 PHE 0.015 0.001 PHE B 509 TRP 0.012 0.001 TRP B 452 HIS 0.002 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 7402) covalent geometry : angle 0.53314 (10132) hydrogen bonds : bond 0.04019 ( 330) hydrogen bonds : angle 4.01915 ( 990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.260 Fit side-chains REVERT: A 104 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.7900 (p) REVERT: A 131 LEU cc_start: 0.7944 (tp) cc_final: 0.7461 (tp) REVERT: A 330 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7282 (mp) REVERT: B 104 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.7895 (p) REVERT: B 115 VAL cc_start: 0.8005 (p) cc_final: 0.7776 (t) REVERT: B 131 LEU cc_start: 0.7909 (tp) cc_final: 0.7444 (tp) REVERT: B 330 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7260 (mp) REVERT: B 350 LYS cc_start: 0.8018 (mmmm) cc_final: 0.7808 (mtpp) outliers start: 14 outliers final: 8 residues processed: 66 average time/residue: 0.4342 time to fit residues: 30.8657 Evaluate side-chains 67 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.091478 restraints weight = 8701.239| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.58 r_work: 0.2850 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7402 Z= 0.107 Angle : 0.546 6.989 10132 Z= 0.272 Chirality : 0.039 0.117 1216 Planarity : 0.004 0.040 1212 Dihedral : 5.901 40.771 1138 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.54 % Allowed : 14.04 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.28), residues: 942 helix: 0.64 (0.20), residues: 738 sheet: None (None), residues: 0 loop : -1.41 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 259 TYR 0.007 0.001 TYR A 331 PHE 0.015 0.001 PHE B 509 TRP 0.012 0.001 TRP B 452 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 7402) covalent geometry : angle 0.54571 (10132) hydrogen bonds : bond 0.04246 ( 330) hydrogen bonds : angle 4.01463 ( 990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.247 Fit side-chains REVERT: A 104 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.7910 (p) REVERT: A 131 LEU cc_start: 0.7917 (tp) cc_final: 0.7435 (tp) REVERT: A 330 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7287 (mp) REVERT: B 104 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.7915 (p) REVERT: B 115 VAL cc_start: 0.8006 (p) cc_final: 0.7774 (t) REVERT: B 131 LEU cc_start: 0.7911 (tp) cc_final: 0.7452 (tp) REVERT: B 330 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7267 (mp) outliers start: 19 outliers final: 10 residues processed: 65 average time/residue: 0.3531 time to fit residues: 25.1202 Evaluate side-chains 66 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.112086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.089835 restraints weight = 8681.783| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.56 r_work: 0.2827 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7402 Z= 0.121 Angle : 0.574 7.039 10132 Z= 0.286 Chirality : 0.041 0.121 1216 Planarity : 0.005 0.042 1212 Dihedral : 6.017 41.890 1138 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.14 % Allowed : 14.30 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.28), residues: 942 helix: 0.57 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -1.42 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 259 TYR 0.008 0.001 TYR A 331 PHE 0.015 0.001 PHE B 509 TRP 0.011 0.001 TRP A 452 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7402) covalent geometry : angle 0.57360 (10132) hydrogen bonds : bond 0.04809 ( 330) hydrogen bonds : angle 4.08178 ( 990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.272 Fit side-chains REVERT: A 104 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.7918 (p) REVERT: A 131 LEU cc_start: 0.7998 (tp) cc_final: 0.7528 (tp) REVERT: A 330 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7323 (mp) REVERT: B 104 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.7928 (p) REVERT: B 131 LEU cc_start: 0.7974 (tp) cc_final: 0.7505 (tp) REVERT: B 330 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7297 (mp) outliers start: 16 outliers final: 10 residues processed: 69 average time/residue: 0.4409 time to fit residues: 32.7706 Evaluate side-chains 72 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 509 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.088591 restraints weight = 8767.077| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.58 r_work: 0.2806 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7402 Z= 0.142 Angle : 0.611 6.995 10132 Z= 0.305 Chirality : 0.042 0.128 1216 Planarity : 0.005 0.044 1212 Dihedral : 6.212 44.540 1138 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.01 % Allowed : 14.30 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.28), residues: 942 helix: 0.45 (0.20), residues: 738 sheet: None (None), residues: 0 loop : -1.41 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 259 TYR 0.009 0.001 TYR B 331 PHE 0.015 0.002 PHE A 509 TRP 0.010 0.001 TRP A 308 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7402) covalent geometry : angle 0.61095 (10132) hydrogen bonds : bond 0.05480 ( 330) hydrogen bonds : angle 4.18028 ( 990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.65 seconds wall clock time: 37 minutes 44.05 seconds (2264.05 seconds total)