Starting phenix.real_space_refine on Sun Aug 24 00:57:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8igg_35432/08_2025/8igg_35432.cif Found real_map, /net/cci-nas-00/data/ceres_data/8igg_35432/08_2025/8igg_35432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8igg_35432/08_2025/8igg_35432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8igg_35432/08_2025/8igg_35432.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8igg_35432/08_2025/8igg_35432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8igg_35432/08_2025/8igg_35432.map" } resolution = 4.09 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= 0.000 sd= 0.004 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 50 5.16 5 C 10002 2.51 5 N 2892 2.21 5 O 3054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 15998 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 4014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4014 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3985 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 23, 'TRANS': 487} Chain breaks: 3 Restraints were copied for chains: B, C Time building chain proxies: 6.05, per 1000 atoms: 0.38 Number of scatterers: 15998 At special positions: 0 Unit cell: (148.75, 126.25, 87.5, 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 50 16.00 O 3054 8.00 N 2892 7.00 C 10002 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: 1.42 Conformation dependent library (CDL) restraints added in 744.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 22 sheets defined 42.2% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'E' and resid 50 through 55 removed outlier: 3.908A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR E 55 " --> pdb=" O ASN E 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 50 through 55' Processing helix chain 'E' and resid 65 through 84 removed outlier: 3.826A pdb=" N GLU E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.846A pdb=" N HIS E 101 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 102' Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 198 through 201 removed outlier: 3.513A pdb=" N ASP E 201 " --> pdb=" O VAL E 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 201' Processing helix chain 'E' and resid 202 through 226 Processing helix chain 'E' and resid 231 through 235 Processing helix chain 'E' and resid 302 through 311 removed outlier: 3.892A pdb=" N GLN E 306 " --> pdb=" O THR E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 351 Processing helix chain 'E' and resid 352 through 367 removed outlier: 4.432A pdb=" N SER E 356 " --> pdb=" O ALA E 353 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLY E 359 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TRP E 362 " --> pdb=" O GLY E 359 " (cutoff:3.500A) Proline residue: E 365 - end of helix Processing helix chain 'E' and resid 378 through 384 removed outlier: 3.565A pdb=" N ALA E 381 " --> pdb=" O ASP E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 410 Processing helix chain 'E' and resid 428 through 439 removed outlier: 3.848A pdb=" N LEU E 434 " --> pdb=" O GLN E 430 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN E 435 " --> pdb=" O MET E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 460 Processing helix chain 'E' and resid 462 through 466 Processing helix chain 'E' and resid 497 through 499 No H-bonds generated for 'chain 'E' and resid 497 through 499' Processing helix chain 'E' and resid 501 through 509 Processing helix chain 'E' and resid 511 through 523 Processing helix chain 'E' and resid 528 through 543 Processing helix chain 'E' and resid 560 through 576 removed outlier: 3.656A pdb=" N ILE E 564 " --> pdb=" O ASN E 560 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG E 569 " --> pdb=" O GLU E 565 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU E 576 " --> pdb=" O ALA E 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 82 Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.616A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 202 through 222 removed outlier: 3.546A pdb=" N LEU A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.245A pdb=" N LYS A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 237' Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.546A pdb=" N PHE A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.866A pdb=" N ALA A 361 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TRP A 362 " --> pdb=" O GLY A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 removed outlier: 4.031A pdb=" N ALA A 381 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 Processing helix chain 'A' and resid 428 through 439 removed outlier: 4.804A pdb=" N LEU A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.983A pdb=" N PHE A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.614A pdb=" N LEU A 499 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 528 through 544 removed outlier: 3.684A pdb=" N ARG A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 575 removed outlier: 3.753A pdb=" N ILE A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.618A pdb=" N ASN A 601 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.908A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 55 " --> pdb=" O ASN B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 55' Processing helix chain 'B' and resid 65 through 84 removed outlier: 3.826A pdb=" N GLU B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.846A pdb=" N HIS B 101 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 102 " --> pdb=" O ASP B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 163 through 179 Processing helix chain 'B' and resid 198 through 201 removed outlier: 3.513A pdb=" N ASP B 201 " --> pdb=" O VAL B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 202 through 226 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 302 through 311 removed outlier: 3.892A pdb=" N GLN B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 352 through 367 removed outlier: 4.432A pdb=" N SER B 356 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLY B 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TRP B 362 " --> pdb=" O GLY B 359 " (cutoff:3.500A) Proline residue: B 365 - end of helix Processing helix chain 'B' and resid 378 through 384 removed outlier: 3.565A pdb=" N ALA B 381 " --> pdb=" O ASP B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 410 Processing helix chain 'B' and resid 428 through 439 removed outlier: 3.848A pdb=" N LEU B 434 " --> pdb=" O GLN B 430 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 435 " --> pdb=" O MET B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 501 through 509 Processing helix chain 'B' and resid 511 through 523 Processing helix chain 'B' and resid 528 through 543 Processing helix chain 'B' and resid 560 through 576 removed outlier: 3.656A pdb=" N ILE B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 82 Processing helix chain 'C' and resid 157 through 162 removed outlier: 3.616A pdb=" N PHE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 Processing helix chain 'C' and resid 202 through 222 removed outlier: 3.546A pdb=" N LEU C 221 " --> pdb=" O CYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.245A pdb=" N LYS C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 237' Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.546A pdb=" N PHE C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 364 removed outlier: 3.866A pdb=" N ALA C 361 " --> pdb=" O HIS C 358 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TRP C 362 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 386 removed outlier: 4.031A pdb=" N ALA C 381 " --> pdb=" O ASP C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 412 Processing helix chain 'C' and resid 428 through 439 removed outlier: 4.804A pdb=" N LEU C 434 " --> pdb=" O GLN C 430 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN C 435 " --> pdb=" O MET C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 457 Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.983A pdb=" N PHE C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 499 removed outlier: 3.614A pdb=" N LEU C 499 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 514 through 523 Processing helix chain 'C' and resid 528 through 544 removed outlier: 3.684A pdb=" N ARG C 532 " --> pdb=" O HIS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 removed outlier: 3.753A pdb=" N ILE C 564 " --> pdb=" O ASN C 560 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 601 removed outlier: 3.618A pdb=" N ASN C 601 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'E' and resid 92 through 93 removed outlier: 9.018A pdb=" N PHE E 191 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 139 through 145 Processing sheet with id=AA4, first strand: chain 'E' and resid 248 through 249 removed outlier: 6.858A pdb=" N ILE E 266 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA E 294 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL E 268 " --> pdb=" O GLN E 292 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN E 292 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR E 270 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA E 294 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP E 331 " --> pdb=" O ASP E 421 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ASN E 423 " --> pdb=" O ASP E 331 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE E 418 " --> pdb=" O TYR E 559 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR E 550 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN E 486 " --> pdb=" O TYR E 550 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY E 552 " --> pdb=" O LEU E 484 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 475 through 476 removed outlier: 5.175A pdb=" N PHE E 418 " --> pdb=" O TYR E 559 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP E 331 " --> pdb=" O ASP E 421 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ASN E 423 " --> pdb=" O ASP E 331 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA E 294 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR E 270 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN E 292 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL E 268 " --> pdb=" O GLN E 292 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA E 294 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE E 266 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU E 243 " --> pdb=" O THR E 579 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 254 through 255 Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 96 removed outlier: 4.116A pdb=" N SER A 106 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 127 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE A 191 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 242 through 249 removed outlier: 4.244A pdb=" N THR A 242 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG A 272 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS A 289 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA A 294 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP A 323 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL A 417 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA A 325 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN A 419 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 327 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP A 421 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE A 329 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN A 423 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ASP A 331 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE A 418 " --> pdb=" O TYR A 559 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 242 through 249 removed outlier: 4.244A pdb=" N THR A 242 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG A 272 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS A 289 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA A 294 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP A 323 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL A 417 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA A 325 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN A 419 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 327 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP A 421 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE A 329 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN A 423 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ASP A 331 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE A 418 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 484 " --> pdb=" O THR A 551 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AB3, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AB4, first strand: chain 'B' and resid 92 through 93 removed outlier: 9.018A pdb=" N PHE B 191 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 139 through 145 Processing sheet with id=AB6, first strand: chain 'B' and resid 248 through 249 removed outlier: 6.858A pdb=" N ILE B 266 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 294 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 268 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 292 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR B 270 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 294 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP B 331 " --> pdb=" O ASP B 421 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ASN B 423 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE B 418 " --> pdb=" O TYR B 559 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR B 550 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN B 486 " --> pdb=" O TYR B 550 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 552 " --> pdb=" O LEU B 484 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 475 through 476 removed outlier: 5.175A pdb=" N PHE B 418 " --> pdb=" O TYR B 559 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP B 331 " --> pdb=" O ASP B 421 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ASN B 423 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 294 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR B 270 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 292 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 268 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 294 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 266 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 243 " --> pdb=" O THR B 579 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 254 through 255 Processing sheet with id=AB9, first strand: chain 'C' and resid 92 through 96 Processing sheet with id=AC1, first strand: chain 'C' and resid 92 through 96 removed outlier: 4.116A pdb=" N SER C 106 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 127 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE C 191 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 242 through 249 removed outlier: 4.244A pdb=" N THR C 242 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG C 272 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS C 289 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA C 294 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP C 323 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL C 417 " --> pdb=" O TRP C 323 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA C 325 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN C 419 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL C 327 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP C 421 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE C 329 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN C 423 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ASP C 331 " --> pdb=" O ASN C 423 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE C 418 " --> pdb=" O TYR C 559 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 242 through 249 removed outlier: 4.244A pdb=" N THR C 242 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG C 272 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS C 289 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA C 294 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP C 323 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL C 417 " --> pdb=" O TRP C 323 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA C 325 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN C 419 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL C 327 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP C 421 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE C 329 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN C 423 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ASP C 331 " --> pdb=" O ASN C 423 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE C 418 " --> pdb=" O TYR C 559 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 484 " --> pdb=" O THR C 551 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 254 through 255 814 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.10 Time building geometry restraints manager: 1.85 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: 4776 1.33 - 1.45: 2534 1.45 - 1.57: 8892 1.57 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 16294 Sorted by residual: bond pdb=" N VAL A 412 " pdb=" CA VAL A 412 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" N VAL C 412 " pdb=" CA VAL C 412 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" N GLN C 411 " pdb=" CA GLN C 411 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.22e-02 6.72e+03 9.96e+00 bond pdb=" N GLN A 411 " pdb=" CA GLN A 411 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.22e-02 6.72e+03 9.96e+00 bond pdb=" N MET A 408 " pdb=" CA MET A 408 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.53e+00 ... (remaining 16289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 21664 1.85 - 3.69: 362 3.69 - 5.54: 52 5.54 - 7.38: 20 7.38 - 9.23: 8 Bond angle restraints: 22106 Sorted by residual: angle pdb=" N GLN A 411 " pdb=" CA GLN A 411 " pdb=" C GLN A 411 " ideal model delta sigma weight residual 111.56 118.29 -6.73 1.53e+00 4.27e-01 1.93e+01 angle pdb=" N GLN C 411 " pdb=" CA GLN C 411 " pdb=" C GLN C 411 " ideal model delta sigma weight residual 111.56 118.29 -6.73 1.53e+00 4.27e-01 1.93e+01 angle pdb=" CA GLN C 411 " pdb=" C GLN C 411 " pdb=" O GLN C 411 " ideal model delta sigma weight residual 120.56 116.00 4.56 1.21e+00 6.83e-01 1.42e+01 angle pdb=" CA GLN A 411 " pdb=" C GLN A 411 " pdb=" O GLN A 411 " ideal model delta sigma weight residual 120.56 116.00 4.56 1.21e+00 6.83e-01 1.42e+01 angle pdb=" N GLN C 406 " pdb=" CA GLN C 406 " pdb=" C GLN C 406 " ideal model delta sigma weight residual 111.03 107.03 4.00 1.11e+00 8.12e-01 1.30e+01 ... (remaining 22101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8750 17.93 - 35.86: 852 35.86 - 53.79: 142 53.79 - 71.72: 32 71.72 - 89.65: 30 Dihedral angle restraints: 9806 sinusoidal: 3928 harmonic: 5878 Sorted by residual: dihedral pdb=" CB GLU E 573 " pdb=" CG GLU E 573 " pdb=" CD GLU E 573 " pdb=" OE1 GLU E 573 " ideal model delta sinusoidal sigma weight residual 0.00 -89.52 89.52 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 573 " pdb=" CG GLU B 573 " pdb=" CD GLU B 573 " pdb=" OE1 GLU B 573 " ideal model delta sinusoidal sigma weight residual 0.00 -89.52 89.52 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 76 " pdb=" CD ARG B 76 " pdb=" NE ARG B 76 " pdb=" CZ ARG B 76 " ideal model delta sinusoidal sigma weight residual -90.00 -134.44 44.44 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 9803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1816 0.040 - 0.081: 426 0.081 - 0.121: 176 0.121 - 0.161: 24 0.161 - 0.202: 10 Chirality restraints: 2452 Sorted by residual: chirality pdb=" CA GLN C 406 " pdb=" N GLN C 406 " pdb=" C GLN C 406 " pdb=" CB GLN C 406 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLN A 406 " pdb=" N GLN A 406 " pdb=" C GLN A 406 " pdb=" CB GLN A 406 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLN A 411 " pdb=" N GLN A 411 " pdb=" C GLN A 411 " pdb=" CB GLN A 411 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 2449 not shown) Planarity restraints: 2970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 405 " 0.022 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C GLY A 405 " -0.078 2.00e-02 2.50e+03 pdb=" O GLY A 405 " 0.030 2.00e-02 2.50e+03 pdb=" N GLN A 406 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 405 " -0.022 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C GLY C 405 " 0.078 2.00e-02 2.50e+03 pdb=" O GLY C 405 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN C 406 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 367 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO E 368 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 368 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 368 " -0.024 5.00e-02 4.00e+02 ... (remaining 2967 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 440 2.70 - 3.25: 16556 3.25 - 3.80: 24249 3.80 - 4.35: 30313 4.35 - 4.90: 49078 Nonbonded interactions: 120636 Sorted by model distance: nonbonded pdb=" O ASP B 581 " pdb=" OD1 ASN B 582 " model vdw 2.146 3.040 nonbonded pdb=" O ASP E 581 " pdb=" OD1 ASN E 582 " model vdw 2.146 3.040 nonbonded pdb=" OG1 THR A 270 " pdb=" OD1 ASN A 291 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR C 270 " pdb=" OD1 ASN C 291 " model vdw 2.195 3.040 nonbonded pdb=" OD1 ASN A 595 " pdb=" OH TYR B 519 " model vdw 2.209 3.040 ... (remaining 120631 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: 0.03 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'B' } ncs_group { reference = chain 'A' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.680 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.003 0.041 16294 Z= 0.141 Angle : 0.611 9.230 22106 Z= 0.319 Chirality : 0.043 0.202 2452 Planarity : 0.003 0.045 2970 Dihedral : 15.139 89.654 6006 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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 aren not related in a simple way. whole: -0.07 (0.20), residues: 2026 helix: 1.05 (0.20), residues: 714 sheet: -0.24 (0.27), residues: 392 loop : -0.79 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 541 TYR 0.014 0.001 TYR C 570 PHE 0.018 0.001 PHE C 404 TRP 0.022 0.001 TRP C 487 HIS 0.002 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00254 (16294) covalent geometry : angle 0.61053 (22106) hydrogen bonds : bond 0.15155 ( 704) hydrogen bonds : angle 6.38581 ( 2184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 129 LEU cc_start: 0.9502 (mp) cc_final: 0.9248 (mt) REVERT: E 436 LEU cc_start: 0.8781 (mp) cc_final: 0.8576 (mp) REVERT: E 505 LEU cc_start: 0.8814 (tp) cc_final: 0.8497 (tp) REVERT: A 256 ASP cc_start: 0.7632 (p0) cc_final: 0.7378 (p0) REVERT: A 432 ASP cc_start: 0.7885 (m-30) cc_final: 0.7352 (m-30) REVERT: B 129 LEU cc_start: 0.9502 (mp) cc_final: 0.9247 (mt) REVERT: B 436 LEU cc_start: 0.8779 (mp) cc_final: 0.8574 (mp) REVERT: B 505 LEU cc_start: 0.8814 (tp) cc_final: 0.8499 (tp) REVERT: C 256 ASP cc_start: 0.7634 (p0) cc_final: 0.7381 (p0) REVERT: C 432 ASP cc_start: 0.7881 (m-30) cc_final: 0.7349 (m-30) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1173 time to fit residues: 65.1411 Evaluate side-chains 276 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 313 ASN E 533 ASN A 279 GLN A 411 GLN A 413 GLN B 313 ASN B 533 ASN C 411 GLN C 413 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.107306 restraints weight = 30926.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.110520 restraints weight = 18325.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112701 restraints weight = 12779.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114261 restraints weight = 9954.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115175 restraints weight = 8334.701| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16294 Z= 0.117 Angle : 0.547 7.900 22106 Z= 0.275 Chirality : 0.042 0.174 2452 Planarity : 0.004 0.042 2970 Dihedral : 3.674 13.747 2208 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.29 % Rotamer: Outliers : 0.18 % Allowed : 5.56 % Favored : 94.27 % 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 aren not related in a simple way. whole: -0.00 (0.20), residues: 2026 helix: 1.10 (0.20), residues: 732 sheet: -0.33 (0.27), residues: 402 loop : -0.70 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 497 TYR 0.014 0.001 TYR B 559 PHE 0.009 0.001 PHE E 311 TRP 0.014 0.001 TRP A 487 HIS 0.002 0.001 HIS C 255 Details of bonding type rmsd covalent geometry : bond 0.00254 (16294) covalent geometry : angle 0.54716 (22106) hydrogen bonds : bond 0.03168 ( 704) hydrogen bonds : angle 4.28602 ( 2184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 346 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 295 MET cc_start: 0.7993 (ptt) cc_final: 0.7654 (ptt) REVERT: E 314 GLN cc_start: 0.7987 (tp-100) cc_final: 0.7642 (mt0) REVERT: E 384 TRP cc_start: 0.8284 (m100) cc_final: 0.7609 (m100) REVERT: E 425 MET cc_start: 0.8575 (tpp) cc_final: 0.7831 (mpp) REVERT: E 436 LEU cc_start: 0.8780 (mp) cc_final: 0.8415 (mp) REVERT: E 505 LEU cc_start: 0.8891 (tp) cc_final: 0.8580 (tp) REVERT: A 256 ASP cc_start: 0.7686 (p0) cc_final: 0.7285 (p0) REVERT: A 408 MET cc_start: 0.8875 (tpp) cc_final: 0.7993 (tpp) REVERT: A 432 ASP cc_start: 0.7978 (m-30) cc_final: 0.7541 (m-30) REVERT: A 492 GLU cc_start: 0.7281 (pm20) cc_final: 0.6611 (pm20) REVERT: B 295 MET cc_start: 0.7990 (ptt) cc_final: 0.7645 (ptt) REVERT: B 314 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7642 (mt0) REVERT: B 384 TRP cc_start: 0.8286 (m100) cc_final: 0.7605 (m100) REVERT: B 425 MET cc_start: 0.8583 (tpp) cc_final: 0.7842 (mpp) REVERT: B 436 LEU cc_start: 0.8784 (mp) cc_final: 0.8421 (mp) REVERT: B 505 LEU cc_start: 0.8894 (tp) cc_final: 0.8583 (tp) REVERT: C 256 ASP cc_start: 0.7688 (p0) cc_final: 0.7287 (p0) REVERT: C 408 MET cc_start: 0.8876 (tpp) cc_final: 0.7997 (tpp) REVERT: C 432 ASP cc_start: 0.7975 (m-30) cc_final: 0.7542 (m-30) REVERT: C 492 GLU cc_start: 0.7281 (pm20) cc_final: 0.6611 (pm20) outliers start: 3 outliers final: 0 residues processed: 346 average time/residue: 0.1119 time to fit residues: 60.3339 Evaluate side-chains 274 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 66 optimal weight: 0.0970 chunk 119 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN A 472 GLN C 445 GLN C 472 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.102869 restraints weight = 31580.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105940 restraints weight = 18897.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.108050 restraints weight = 13291.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109542 restraints weight = 10417.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110578 restraints weight = 8753.356| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16294 Z= 0.178 Angle : 0.588 8.822 22106 Z= 0.298 Chirality : 0.043 0.159 2452 Planarity : 0.004 0.044 2970 Dihedral : 3.942 14.586 2208 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % 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 aren not related in a simple way. whole: -0.08 (0.20), residues: 2026 helix: 1.07 (0.20), residues: 732 sheet: -0.36 (0.26), residues: 406 loop : -0.79 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 497 TYR 0.020 0.002 TYR C 570 PHE 0.015 0.001 PHE E 296 TRP 0.021 0.002 TRP A 487 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00400 (16294) covalent geometry : angle 0.58845 (22106) hydrogen bonds : bond 0.03382 ( 704) hydrogen bonds : angle 4.32374 ( 2184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 314 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7891 (tp-100) REVERT: E 384 TRP cc_start: 0.8419 (m100) cc_final: 0.7631 (m100) REVERT: E 425 MET cc_start: 0.8674 (tpp) cc_final: 0.7891 (mpp) REVERT: E 505 LEU cc_start: 0.8785 (tp) cc_final: 0.8308 (tp) REVERT: A 218 ASP cc_start: 0.7862 (t70) cc_final: 0.7566 (t0) REVERT: A 256 ASP cc_start: 0.7713 (p0) cc_final: 0.7334 (p0) REVERT: A 408 MET cc_start: 0.9251 (tpp) cc_final: 0.8628 (tpp) REVERT: A 412 VAL cc_start: 0.9303 (t) cc_final: 0.9055 (m) REVERT: A 432 ASP cc_start: 0.8038 (m-30) cc_final: 0.7751 (m-30) REVERT: A 492 GLU cc_start: 0.7358 (pm20) cc_final: 0.6524 (pm20) REVERT: B 314 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7898 (tp-100) REVERT: B 384 TRP cc_start: 0.8423 (m100) cc_final: 0.7632 (m100) REVERT: B 425 MET cc_start: 0.8669 (tpp) cc_final: 0.7892 (mpp) REVERT: B 505 LEU cc_start: 0.8783 (tp) cc_final: 0.8307 (tp) REVERT: C 218 ASP cc_start: 0.7865 (t70) cc_final: 0.7566 (t0) REVERT: C 256 ASP cc_start: 0.7718 (p0) cc_final: 0.7340 (p0) REVERT: C 408 MET cc_start: 0.9249 (tpp) cc_final: 0.8631 (tpp) REVERT: C 412 VAL cc_start: 0.9302 (t) cc_final: 0.9056 (m) REVERT: C 432 ASP cc_start: 0.8042 (m-30) cc_final: 0.7751 (m-30) REVERT: C 492 GLU cc_start: 0.7352 (pm20) cc_final: 0.6523 (pm20) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.1103 time to fit residues: 55.5439 Evaluate side-chains 266 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 0.0770 chunk 152 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 chunk 185 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 overall best weight: 1.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.105461 restraints weight = 31161.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108609 restraints weight = 18496.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110773 restraints weight = 12942.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112236 restraints weight = 10073.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113297 restraints weight = 8479.514| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16294 Z= 0.127 Angle : 0.565 8.452 22106 Z= 0.283 Chirality : 0.042 0.174 2452 Planarity : 0.003 0.041 2970 Dihedral : 3.860 14.307 2208 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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 aren not related in a simple way. whole: -0.11 (0.20), residues: 2026 helix: 1.02 (0.20), residues: 732 sheet: -0.24 (0.27), residues: 392 loop : -0.85 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 497 TYR 0.021 0.002 TYR A 570 PHE 0.011 0.001 PHE A 167 TRP 0.019 0.001 TRP A 487 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00279 (16294) covalent geometry : angle 0.56489 (22106) hydrogen bonds : bond 0.03023 ( 704) hydrogen bonds : angle 4.16247 ( 2184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 314 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7868 (tp-100) REVERT: E 384 TRP cc_start: 0.8340 (m100) cc_final: 0.7594 (m100) REVERT: E 422 LEU cc_start: 0.8279 (mt) cc_final: 0.7793 (pp) REVERT: E 436 LEU cc_start: 0.8756 (mp) cc_final: 0.8545 (mt) REVERT: E 505 LEU cc_start: 0.8806 (tp) cc_final: 0.8272 (tp) REVERT: A 256 ASP cc_start: 0.7667 (p0) cc_final: 0.7233 (p0) REVERT: A 408 MET cc_start: 0.9230 (tpp) cc_final: 0.8152 (tpp) REVERT: A 412 VAL cc_start: 0.9299 (t) cc_final: 0.9028 (m) REVERT: A 432 ASP cc_start: 0.7915 (m-30) cc_final: 0.7445 (m-30) REVERT: A 492 GLU cc_start: 0.7386 (pm20) cc_final: 0.6525 (pm20) REVERT: B 314 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7875 (tp-100) REVERT: B 384 TRP cc_start: 0.8344 (m100) cc_final: 0.7594 (m100) REVERT: B 422 LEU cc_start: 0.8279 (mt) cc_final: 0.7797 (pp) REVERT: B 436 LEU cc_start: 0.8757 (mp) cc_final: 0.8543 (mt) REVERT: B 505 LEU cc_start: 0.8806 (tp) cc_final: 0.8276 (tp) REVERT: C 256 ASP cc_start: 0.7667 (p0) cc_final: 0.7235 (p0) REVERT: C 408 MET cc_start: 0.9225 (tpp) cc_final: 0.8471 (tpp) REVERT: C 412 VAL cc_start: 0.9295 (t) cc_final: 0.9021 (m) REVERT: C 432 ASP cc_start: 0.7907 (m-30) cc_final: 0.7439 (m-30) REVERT: C 492 GLU cc_start: 0.7387 (pm20) cc_final: 0.6528 (pm20) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.1195 time to fit residues: 61.3839 Evaluate side-chains 277 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 149 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 190 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN C 445 GLN ** C 472 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 = 0.3559 r_free = 0.3559 target = 0.132471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110794 restraints weight = 30352.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113971 restraints weight = 18023.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116189 restraints weight = 12552.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117721 restraints weight = 9723.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118665 restraints weight = 8097.804| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16294 Z= 0.131 Angle : 0.569 8.255 22106 Z= 0.285 Chirality : 0.043 0.177 2452 Planarity : 0.004 0.042 2970 Dihedral : 3.861 16.293 2208 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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 aren not related in a simple way. whole: -0.11 (0.20), residues: 2026 helix: 1.05 (0.20), residues: 732 sheet: -0.40 (0.26), residues: 396 loop : -0.80 (0.23), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 56 TYR 0.016 0.001 TYR A 543 PHE 0.012 0.001 PHE C 167 TRP 0.021 0.002 TRP A 487 HIS 0.002 0.000 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00293 (16294) covalent geometry : angle 0.56913 (22106) hydrogen bonds : bond 0.03006 ( 704) hydrogen bonds : angle 4.08825 ( 2184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 314 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7813 (tp-100) REVERT: E 384 TRP cc_start: 0.8317 (m100) cc_final: 0.7645 (m100) REVERT: E 425 MET cc_start: 0.8633 (tpp) cc_final: 0.7858 (mpp) REVERT: E 505 LEU cc_start: 0.8757 (tp) cc_final: 0.8403 (tp) REVERT: A 108 LEU cc_start: 0.9106 (tp) cc_final: 0.8815 (tt) REVERT: A 218 ASP cc_start: 0.7886 (t70) cc_final: 0.7592 (t0) REVERT: A 256 ASP cc_start: 0.7645 (p0) cc_final: 0.7216 (p0) REVERT: A 408 MET cc_start: 0.9224 (tpp) cc_final: 0.8470 (tpp) REVERT: A 412 VAL cc_start: 0.9326 (t) cc_final: 0.9061 (m) REVERT: A 432 ASP cc_start: 0.7894 (m-30) cc_final: 0.7620 (m-30) REVERT: A 492 GLU cc_start: 0.7387 (pm20) cc_final: 0.6567 (pm20) REVERT: B 314 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7834 (tp-100) REVERT: B 384 TRP cc_start: 0.8317 (m100) cc_final: 0.7646 (m100) REVERT: B 425 MET cc_start: 0.8636 (tpp) cc_final: 0.7864 (mpp) REVERT: B 505 LEU cc_start: 0.8759 (tp) cc_final: 0.8409 (tp) REVERT: C 108 LEU cc_start: 0.9109 (tp) cc_final: 0.8819 (tt) REVERT: C 218 ASP cc_start: 0.7901 (t70) cc_final: 0.7606 (t0) REVERT: C 256 ASP cc_start: 0.7640 (p0) cc_final: 0.7211 (p0) REVERT: C 408 MET cc_start: 0.9223 (tpp) cc_final: 0.8470 (tpp) REVERT: C 412 VAL cc_start: 0.9325 (t) cc_final: 0.9060 (m) REVERT: C 432 ASP cc_start: 0.7893 (m-30) cc_final: 0.7619 (m-30) REVERT: C 492 GLU cc_start: 0.7383 (pm20) cc_final: 0.6566 (pm20) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1204 time to fit residues: 60.0533 Evaluate side-chains 276 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 149 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 155 optimal weight: 0.5980 chunk 73 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 197 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113875 restraints weight = 30141.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117046 restraints weight = 17866.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119359 restraints weight = 12477.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120933 restraints weight = 9623.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122019 restraints weight = 7958.781| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16294 Z= 0.100 Angle : 0.559 8.332 22106 Z= 0.275 Chirality : 0.042 0.176 2452 Planarity : 0.004 0.049 2970 Dihedral : 3.672 15.431 2208 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.02 (0.20), residues: 2026 helix: 1.12 (0.20), residues: 732 sheet: -0.19 (0.27), residues: 388 loop : -0.83 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 56 TYR 0.010 0.001 TYR E 559 PHE 0.012 0.001 PHE A 283 TRP 0.019 0.001 TRP A 487 HIS 0.002 0.000 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00215 (16294) covalent geometry : angle 0.55862 (22106) hydrogen bonds : bond 0.02688 ( 704) hydrogen bonds : angle 3.91797 ( 2184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 314 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7791 (tp-100) REVERT: E 384 TRP cc_start: 0.8271 (m100) cc_final: 0.7562 (m100) REVERT: E 425 MET cc_start: 0.8618 (tpp) cc_final: 0.7804 (mpp) REVERT: E 505 LEU cc_start: 0.8869 (tp) cc_final: 0.8249 (tp) REVERT: E 557 CYS cc_start: 0.8078 (p) cc_final: 0.7873 (p) REVERT: A 256 ASP cc_start: 0.7591 (p0) cc_final: 0.7076 (p0) REVERT: A 408 MET cc_start: 0.9171 (tpp) cc_final: 0.8378 (tpp) REVERT: A 412 VAL cc_start: 0.9310 (t) cc_final: 0.9044 (m) REVERT: A 432 ASP cc_start: 0.8064 (m-30) cc_final: 0.7775 (m-30) REVERT: A 492 GLU cc_start: 0.7325 (pm20) cc_final: 0.6588 (pm20) REVERT: B 314 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7808 (tp-100) REVERT: B 384 TRP cc_start: 0.8272 (m100) cc_final: 0.7561 (m100) REVERT: B 425 MET cc_start: 0.8612 (tpp) cc_final: 0.7806 (mpp) REVERT: B 505 LEU cc_start: 0.8872 (tp) cc_final: 0.8251 (tp) REVERT: B 557 CYS cc_start: 0.8078 (p) cc_final: 0.7873 (p) REVERT: C 256 ASP cc_start: 0.7588 (p0) cc_final: 0.7073 (p0) REVERT: C 408 MET cc_start: 0.9169 (tpp) cc_final: 0.8384 (tpp) REVERT: C 412 VAL cc_start: 0.9306 (t) cc_final: 0.9041 (m) REVERT: C 432 ASP cc_start: 0.8059 (m-30) cc_final: 0.7772 (m-30) REVERT: C 492 GLU cc_start: 0.7333 (pm20) cc_final: 0.6594 (pm20) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1224 time to fit residues: 64.8597 Evaluate side-chains 274 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 159 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 202 optimal weight: 0.2980 chunk 96 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 271 GLN A 117 ASN A 445 GLN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN C 117 ASN ** C 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.130199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108395 restraints weight = 30500.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111444 restraints weight = 18294.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113629 restraints weight = 12866.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115144 restraints weight = 10013.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116201 restraints weight = 8373.254| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16294 Z= 0.152 Angle : 0.596 8.302 22106 Z= 0.298 Chirality : 0.043 0.153 2452 Planarity : 0.004 0.041 2970 Dihedral : 3.875 16.212 2208 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.50 % Favored : 92.40 % Rotamer: Outliers : 0.12 % Allowed : 1.00 % Favored : 98.88 % 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 aren not related in a simple way. whole: -0.20 (0.20), residues: 2026 helix: 0.93 (0.20), residues: 744 sheet: -0.28 (0.27), residues: 390 loop : -0.93 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 56 TYR 0.015 0.002 TYR B 559 PHE 0.014 0.001 PHE A 283 TRP 0.028 0.001 TRP A 487 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00343 (16294) covalent geometry : angle 0.59619 (22106) hydrogen bonds : bond 0.03060 ( 704) hydrogen bonds : angle 4.13953 ( 2184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 322 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 314 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7921 (tp-100) REVERT: E 384 TRP cc_start: 0.8354 (m100) cc_final: 0.7679 (m100) REVERT: E 505 LEU cc_start: 0.8741 (tp) cc_final: 0.8375 (tp) REVERT: A 84 GLN cc_start: 0.7630 (tp40) cc_final: 0.7414 (tp40) REVERT: A 256 ASP cc_start: 0.7606 (p0) cc_final: 0.7179 (p0) REVERT: A 408 MET cc_start: 0.9168 (tpp) cc_final: 0.8424 (tpp) REVERT: A 412 VAL cc_start: 0.9378 (t) cc_final: 0.9119 (m) REVERT: A 432 ASP cc_start: 0.8267 (m-30) cc_final: 0.7905 (m-30) REVERT: B 314 GLN cc_start: 0.8177 (tp-100) cc_final: 0.7941 (tp-100) REVERT: B 384 TRP cc_start: 0.8352 (m100) cc_final: 0.7680 (m100) REVERT: B 505 LEU cc_start: 0.8743 (tp) cc_final: 0.8380 (tp) REVERT: C 84 GLN cc_start: 0.7624 (tp40) cc_final: 0.7411 (tp40) REVERT: C 256 ASP cc_start: 0.7613 (p0) cc_final: 0.7185 (p0) REVERT: C 408 MET cc_start: 0.9165 (tpp) cc_final: 0.8427 (tpp) REVERT: C 412 VAL cc_start: 0.9375 (t) cc_final: 0.9114 (m) REVERT: C 432 ASP cc_start: 0.8255 (m-30) cc_final: 0.7897 (m-30) outliers start: 2 outliers final: 0 residues processed: 324 average time/residue: 0.1167 time to fit residues: 59.0346 Evaluate side-chains 272 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 143 optimal weight: 2.9990 chunk 116 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112861 restraints weight = 30763.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116021 restraints weight = 18690.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118223 restraints weight = 13191.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119763 restraints weight = 10301.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120840 restraints weight = 8631.028| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16294 Z= 0.106 Angle : 0.575 9.236 22106 Z= 0.285 Chirality : 0.043 0.161 2452 Planarity : 0.003 0.041 2970 Dihedral : 3.700 15.237 2208 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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 aren not related in a simple way. whole: -0.04 (0.20), residues: 2026 helix: 1.10 (0.20), residues: 730 sheet: -0.22 (0.27), residues: 390 loop : -0.83 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 56 TYR 0.013 0.002 TYR E 559 PHE 0.011 0.001 PHE C 283 TRP 0.021 0.001 TRP A 487 HIS 0.002 0.000 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00227 (16294) covalent geometry : angle 0.57496 (22106) hydrogen bonds : bond 0.02717 ( 704) hydrogen bonds : angle 3.90012 ( 2184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7802 (mmtp) REVERT: E 314 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7813 (tp40) REVERT: E 384 TRP cc_start: 0.8266 (m100) cc_final: 0.7595 (m100) REVERT: E 425 MET cc_start: 0.8529 (tpp) cc_final: 0.7708 (mpp) REVERT: E 505 LEU cc_start: 0.8820 (tp) cc_final: 0.8437 (tp) REVERT: A 256 ASP cc_start: 0.7572 (p0) cc_final: 0.7063 (p0) REVERT: A 346 TYR cc_start: 0.8381 (t80) cc_final: 0.8150 (t80) REVERT: A 408 MET cc_start: 0.9156 (tpp) cc_final: 0.8357 (tpp) REVERT: A 412 VAL cc_start: 0.9354 (t) cc_final: 0.9130 (m) REVERT: A 432 ASP cc_start: 0.7748 (m-30) cc_final: 0.7297 (m-30) REVERT: B 246 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7805 (mmtp) REVERT: B 314 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7822 (tp40) REVERT: B 384 TRP cc_start: 0.8265 (m100) cc_final: 0.7595 (m100) REVERT: B 425 MET cc_start: 0.8528 (tpp) cc_final: 0.7715 (mpp) REVERT: B 505 LEU cc_start: 0.8825 (tp) cc_final: 0.8439 (tp) REVERT: C 256 ASP cc_start: 0.7568 (p0) cc_final: 0.7061 (p0) REVERT: C 346 TYR cc_start: 0.8376 (t80) cc_final: 0.8145 (t80) REVERT: C 408 MET cc_start: 0.9154 (tpp) cc_final: 0.8357 (tpp) REVERT: C 412 VAL cc_start: 0.9350 (t) cc_final: 0.9126 (m) REVERT: C 432 ASP cc_start: 0.7752 (m-30) cc_final: 0.7291 (m-30) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1188 time to fit residues: 59.8615 Evaluate side-chains 284 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 38 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114750 restraints weight = 30132.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117936 restraints weight = 18002.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120196 restraints weight = 12558.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121733 restraints weight = 9706.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122813 restraints weight = 8063.354| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16294 Z= 0.110 Angle : 0.588 8.969 22106 Z= 0.290 Chirality : 0.043 0.163 2452 Planarity : 0.003 0.041 2970 Dihedral : 3.694 17.044 2208 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.02 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 aren not related in a simple way. whole: -0.04 (0.20), residues: 2026 helix: 1.10 (0.20), residues: 732 sheet: -0.16 (0.27), residues: 390 loop : -0.85 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 56 TYR 0.018 0.002 TYR E 559 PHE 0.015 0.001 PHE C 74 TRP 0.020 0.001 TRP A 487 HIS 0.002 0.000 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00240 (16294) covalent geometry : angle 0.58835 (22106) hydrogen bonds : bond 0.02752 ( 704) hydrogen bonds : angle 3.88985 ( 2184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7864 (mmtp) REVERT: E 314 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7856 (tp40) REVERT: E 384 TRP cc_start: 0.8255 (m100) cc_final: 0.7603 (m100) REVERT: E 425 MET cc_start: 0.8528 (tpp) cc_final: 0.7738 (mpp) REVERT: E 505 LEU cc_start: 0.8816 (tp) cc_final: 0.8435 (tp) REVERT: A 256 ASP cc_start: 0.7599 (p0) cc_final: 0.7033 (p0) REVERT: A 408 MET cc_start: 0.9151 (tpp) cc_final: 0.8325 (tpp) REVERT: A 412 VAL cc_start: 0.9358 (t) cc_final: 0.9150 (m) REVERT: A 432 ASP cc_start: 0.7825 (m-30) cc_final: 0.7444 (m-30) REVERT: B 246 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7867 (mmtp) REVERT: B 314 GLN cc_start: 0.8098 (tp-100) cc_final: 0.7877 (tp40) REVERT: B 384 TRP cc_start: 0.8252 (m100) cc_final: 0.7600 (m100) REVERT: B 425 MET cc_start: 0.8526 (tpp) cc_final: 0.7737 (mpp) REVERT: B 505 LEU cc_start: 0.8819 (tp) cc_final: 0.8436 (tp) REVERT: C 256 ASP cc_start: 0.7594 (p0) cc_final: 0.7028 (p0) REVERT: C 408 MET cc_start: 0.9149 (tpp) cc_final: 0.8330 (tpp) REVERT: C 412 VAL cc_start: 0.9354 (t) cc_final: 0.9145 (m) REVERT: C 432 ASP cc_start: 0.7823 (m-30) cc_final: 0.7444 (m-30) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1188 time to fit residues: 59.8075 Evaluate side-chains 269 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 26 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114011 restraints weight = 30478.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117197 restraints weight = 18199.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119415 restraints weight = 12698.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120938 restraints weight = 9844.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121965 restraints weight = 8207.340| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16294 Z= 0.109 Angle : 0.582 9.074 22106 Z= 0.285 Chirality : 0.043 0.165 2452 Planarity : 0.003 0.041 2970 Dihedral : 3.654 16.794 2208 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.81 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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 aren not related in a simple way. whole: -0.03 (0.20), residues: 2026 helix: 1.12 (0.20), residues: 732 sheet: -0.16 (0.28), residues: 388 loop : -0.86 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 56 TYR 0.020 0.002 TYR B 559 PHE 0.012 0.001 PHE C 283 TRP 0.023 0.001 TRP A 487 HIS 0.002 0.000 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00237 (16294) covalent geometry : angle 0.58169 (22106) hydrogen bonds : bond 0.02776 ( 704) hydrogen bonds : angle 3.83922 ( 2184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 ASP cc_start: 0.8029 (p0) cc_final: 0.7074 (t0) REVERT: E 129 LEU cc_start: 0.9502 (mp) cc_final: 0.9205 (mt) REVERT: E 246 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7908 (mmtp) REVERT: E 314 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7877 (tp40) REVERT: E 384 TRP cc_start: 0.8278 (m100) cc_final: 0.7615 (m100) REVERT: E 425 MET cc_start: 0.8537 (tpp) cc_final: 0.7728 (mpp) REVERT: E 505 LEU cc_start: 0.8810 (tp) cc_final: 0.8426 (tp) REVERT: A 256 ASP cc_start: 0.7553 (p0) cc_final: 0.7031 (p0) REVERT: A 408 MET cc_start: 0.9147 (tpp) cc_final: 0.8316 (tpp) REVERT: A 412 VAL cc_start: 0.9384 (t) cc_final: 0.9181 (m) REVERT: A 432 ASP cc_start: 0.8087 (m-30) cc_final: 0.7760 (m-30) REVERT: B 90 ASP cc_start: 0.8034 (p0) cc_final: 0.7079 (t0) REVERT: B 129 LEU cc_start: 0.9504 (mp) cc_final: 0.9207 (mt) REVERT: B 246 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7912 (mmtp) REVERT: B 314 GLN cc_start: 0.8107 (tp-100) cc_final: 0.7896 (tp40) REVERT: B 384 TRP cc_start: 0.8275 (m100) cc_final: 0.7612 (m100) REVERT: B 425 MET cc_start: 0.8536 (tpp) cc_final: 0.7730 (mpp) REVERT: B 505 LEU cc_start: 0.8811 (tp) cc_final: 0.8426 (tp) REVERT: C 256 ASP cc_start: 0.7547 (p0) cc_final: 0.7028 (p0) REVERT: C 408 MET cc_start: 0.9143 (tpp) cc_final: 0.8321 (tpp) REVERT: C 412 VAL cc_start: 0.9381 (t) cc_final: 0.9179 (m) REVERT: C 432 ASP cc_start: 0.8086 (m-30) cc_final: 0.7758 (m-30) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1206 time to fit residues: 60.6367 Evaluate side-chains 271 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 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 472 GLN C 445 GLN C 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.130822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109079 restraints weight = 30414.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112195 restraints weight = 18325.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114359 restraints weight = 12847.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115840 restraints weight = 10012.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116841 restraints weight = 8390.680| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16294 Z= 0.141 Angle : 0.600 9.130 22106 Z= 0.300 Chirality : 0.044 0.163 2452 Planarity : 0.004 0.041 2970 Dihedral : 3.788 16.220 2208 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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 aren not related in a simple way. whole: -0.16 (0.20), residues: 2026 helix: 1.02 (0.20), residues: 746 sheet: -0.24 (0.28), residues: 386 loop : -0.96 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 56 TYR 0.025 0.002 TYR B 559 PHE 0.014 0.001 PHE C 230 TRP 0.030 0.002 TRP A 487 HIS 0.003 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00317 (16294) covalent geometry : angle 0.60016 (22106) hydrogen bonds : bond 0.02977 ( 704) hydrogen bonds : angle 3.99216 ( 2184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2419.19 seconds wall clock time: 42 minutes 51.69 seconds (2571.69 seconds total)