Starting phenix.real_space_refine on Sat Jun 14 06:16:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8igg_35432/06_2025/8igg_35432.cif Found real_map, /net/cci-nas-00/data/ceres_data/8igg_35432/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8igg_35432/06_2025/8igg_35432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8igg_35432/06_2025/8igg_35432.map" model { file = "/net/cci-nas-00/data/ceres_data/8igg_35432/06_2025/8igg_35432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8igg_35432/06_2025/8igg_35432.cif" } resolution = 4.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15998 Number of models: 1 Model: "" Number of chains: 2 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 Chain: "B" 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 Restraints were copied for chains: C, E Time building chain proxies: 13.77, per 1000 atoms: 0.86 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: 3.91 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.42 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: 6.14 Time building geometry restraints manager: 4.62 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'E' } 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 44.190 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.001 TRP C 487 HIS 0.002 0.001 HIS C 101 PHE 0.018 0.001 PHE C 404 TYR 0.014 0.001 TYR C 570 ARG 0.005 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.15155 ( 704) hydrogen bonds : angle 6.38581 ( 2184) covalent geometry : bond 0.00254 (16294) covalent geometry : angle 0.61053 (22106) *********************** 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 : 1.806 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: 0.9247 (mt) REVERT: E 436 LEU cc_start: 0.8781 (mp) cc_final: 0.8565 (mt) 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: 0.7379 (p0) REVERT: A 432 ASP cc_start: 0.7885 (m-30) cc_final: 0.7354 (m-30) REVERT: B 129 LEU cc_start: 0.9502 (mp) cc_final: 0.9246 (mt) REVERT: B 436 LEU cc_start: 0.8779 (mp) cc_final: 0.8565 (mt) 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: 0.7350 (m-30) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2390 time to fit residues: 130.3375 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 : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 313 ASN A 411 GLN A 413 GLN B 313 ASN B 533 ASN C 411 GLN C 413 GLN C 445 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109591 restraints weight = 30858.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112641 restraints weight = 18830.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114715 restraints weight = 13394.865| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16294 Z= 0.158 Angle : 0.579 8.145 22106 Z= 0.293 Chirality : 0.043 0.172 2452 Planarity : 0.004 0.043 2970 Dihedral : 3.819 14.292 2208 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.91 % Favored : 92.99 % Rotamer: Outliers : 0.12 % Allowed : 6.26 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 2026 helix: 1.06 (0.20), residues: 732 sheet: -0.40 (0.27), residues: 402 loop : -0.73 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 487 HIS 0.003 0.001 HIS C 255 PHE 0.012 0.001 PHE C 167 TYR 0.015 0.001 TYR B 559 ARG 0.005 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 704) hydrogen bonds : angle 4.40016 ( 2184) covalent geometry : bond 0.00354 (16294) covalent geometry : angle 0.57926 (22106) *********************** 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 328 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 129 LEU cc_start: 0.9512 (mp) cc_final: 0.9311 (mt) REVERT: E 295 MET cc_start: 0.7995 (ptt) cc_final: 0.7752 (ptt) REVERT: E 384 TRP cc_start: 0.8346 (m100) cc_final: 0.7654 (m100) REVERT: E 505 LEU cc_start: 0.8872 (tp) cc_final: 0.8531 (tp) REVERT: A 256 ASP cc_start: 0.7683 (p0) cc_final: 0.7330 (p0) REVERT: A 408 MET cc_start: 0.9090 (tpp) cc_final: 0.8280 (tpp) REVERT: A 432 ASP cc_start: 0.7954 (m-30) cc_final: 0.7507 (m-30) REVERT: B 295 MET cc_start: 0.7989 (ptt) cc_final: 0.7750 (ptt) REVERT: B 384 TRP cc_start: 0.8348 (m100) cc_final: 0.7653 (m100) REVERT: B 505 LEU cc_start: 0.8873 (tp) cc_final: 0.8532 (tp) REVERT: C 256 ASP cc_start: 0.7681 (p0) cc_final: 0.7328 (p0) REVERT: C 408 MET cc_start: 0.9088 (tpp) cc_final: 0.8281 (tpp) REVERT: C 432 ASP cc_start: 0.7947 (m-30) cc_final: 0.7503 (m-30) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.2515 time to fit residues: 125.3835 Evaluate side-chains 265 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 92 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 157 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 279 GLN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 279 GLN ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112095 restraints weight = 30439.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115207 restraints weight = 18548.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117352 restraints weight = 13108.356| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16294 Z= 0.106 Angle : 0.551 8.895 22106 Z= 0.274 Chirality : 0.042 0.160 2452 Planarity : 0.003 0.042 2970 Dihedral : 3.728 13.564 2208 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.29 % Rotamer: Outliers : 0.12 % Allowed : 4.43 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 2026 helix: 1.15 (0.20), residues: 732 sheet: -0.33 (0.27), residues: 404 loop : -0.73 (0.23), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 487 HIS 0.002 0.000 HIS E 101 PHE 0.009 0.001 PHE C 167 TYR 0.020 0.001 TYR C 570 ARG 0.003 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.02964 ( 704) hydrogen bonds : angle 4.05875 ( 2184) covalent geometry : bond 0.00228 (16294) covalent geometry : angle 0.55139 (22106) *********************** 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 353 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 351 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 314 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7644 (mt0) REVERT: E 384 TRP cc_start: 0.8273 (m100) cc_final: 0.7588 (m100) REVERT: E 425 MET cc_start: 0.8562 (tpp) cc_final: 0.7714 (mpp) REVERT: E 505 LEU cc_start: 0.8826 (tp) cc_final: 0.8435 (tp) REVERT: A 218 ASP cc_start: 0.7720 (t70) cc_final: 0.7366 (t0) REVERT: A 256 ASP cc_start: 0.7648 (p0) cc_final: 0.7213 (p0) REVERT: A 432 ASP cc_start: 0.8128 (m-30) cc_final: 0.7801 (m-30) REVERT: A 492 GLU cc_start: 0.7498 (pm20) cc_final: 0.6651 (pm20) REVERT: B 314 GLN cc_start: 0.7876 (tp-100) cc_final: 0.7643 (mt0) REVERT: B 384 TRP cc_start: 0.8277 (m100) cc_final: 0.7584 (m100) REVERT: B 505 LEU cc_start: 0.8830 (tp) cc_final: 0.8442 (tp) REVERT: C 218 ASP cc_start: 0.7727 (t70) cc_final: 0.7375 (t0) REVERT: C 256 ASP cc_start: 0.7651 (p0) cc_final: 0.7247 (p0) REVERT: C 432 ASP cc_start: 0.8126 (m-30) cc_final: 0.7800 (m-30) REVERT: C 492 GLU cc_start: 0.7502 (pm20) cc_final: 0.6652 (pm20) outliers start: 2 outliers final: 0 residues processed: 351 average time/residue: 0.2415 time to fit residues: 130.7030 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 : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 186 optimal weight: 0.1980 chunk 113 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 87 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN C 117 ASN ** 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 = 0.3607 r_free = 0.3607 target = 0.136327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114676 restraints weight = 30302.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117844 restraints weight = 18395.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120065 restraints weight = 12953.780| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16294 Z= 0.101 Angle : 0.548 8.551 22106 Z= 0.270 Chirality : 0.042 0.172 2452 Planarity : 0.003 0.039 2970 Dihedral : 3.628 14.678 2208 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.12 % Allowed : 3.66 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 2026 helix: 1.17 (0.20), residues: 732 sheet: -0.27 (0.27), residues: 402 loop : -0.70 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 487 HIS 0.002 0.000 HIS B 101 PHE 0.010 0.001 PHE C 283 TYR 0.013 0.001 TYR B 166 ARG 0.003 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.02738 ( 704) hydrogen bonds : angle 3.98334 ( 2184) covalent geometry : bond 0.00218 (16294) covalent geometry : angle 0.54843 (22106) *********************** 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 341 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 339 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8256 (m100) cc_final: 0.7586 (m100) REVERT: E 425 MET cc_start: 0.8559 (tpp) cc_final: 0.7709 (mpp) REVERT: E 505 LEU cc_start: 0.8925 (tp) cc_final: 0.8497 (tp) REVERT: A 215 ASN cc_start: 0.8568 (t0) cc_final: 0.8352 (t0) REVERT: A 256 ASP cc_start: 0.7573 (p0) cc_final: 0.7144 (p0) REVERT: A 432 ASP cc_start: 0.8218 (m-30) cc_final: 0.7869 (m-30) REVERT: A 492 GLU cc_start: 0.7302 (pm20) cc_final: 0.6526 (pm20) REVERT: B 384 TRP cc_start: 0.8254 (m100) cc_final: 0.7585 (m100) REVERT: B 425 MET cc_start: 0.8555 (tpp) cc_final: 0.7720 (mpp) REVERT: B 505 LEU cc_start: 0.8928 (tp) cc_final: 0.8501 (tp) REVERT: C 215 ASN cc_start: 0.8580 (t0) cc_final: 0.8364 (t0) REVERT: C 256 ASP cc_start: 0.7588 (p0) cc_final: 0.7131 (p0) REVERT: C 432 ASP cc_start: 0.8207 (m-30) cc_final: 0.7858 (m-30) REVERT: C 492 GLU cc_start: 0.7304 (pm20) cc_final: 0.6526 (pm20) outliers start: 2 outliers final: 0 residues processed: 341 average time/residue: 0.2473 time to fit residues: 129.4892 Evaluate side-chains 280 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 123 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 78 optimal weight: 0.0020 chunk 34 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 40 optimal weight: 0.0370 chunk 109 optimal weight: 5.9990 overall best weight: 1.5670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN ** 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 = 0.3513 r_free = 0.3513 target = 0.129158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106715 restraints weight = 31294.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109866 restraints weight = 18653.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112052 restraints weight = 13018.604| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16294 Z= 0.130 Angle : 0.559 8.372 22106 Z= 0.280 Chirality : 0.043 0.173 2452 Planarity : 0.003 0.039 2970 Dihedral : 3.725 15.182 2208 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 2026 helix: 1.18 (0.20), residues: 730 sheet: -0.26 (0.27), residues: 402 loop : -0.73 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 487 HIS 0.002 0.001 HIS E 101 PHE 0.012 0.001 PHE A 283 TYR 0.021 0.002 TYR C 570 ARG 0.003 0.000 ARG B 497 Details of bonding type rmsd hydrogen bonds : bond 0.02915 ( 704) hydrogen bonds : angle 3.96495 ( 2184) covalent geometry : bond 0.00290 (16294) covalent geometry : angle 0.55897 (22106) *********************** 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: 2 poor density : 321 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8353 (m100) cc_final: 0.7645 (m100) REVERT: E 425 MET cc_start: 0.8622 (tpp) cc_final: 0.7811 (mpp) REVERT: E 505 LEU cc_start: 0.8853 (tp) cc_final: 0.8288 (tp) REVERT: A 256 ASP cc_start: 0.7647 (p0) cc_final: 0.7182 (p0) REVERT: A 408 MET cc_start: 0.9239 (tpp) cc_final: 0.8458 (tpp) REVERT: A 412 VAL cc_start: 0.9332 (t) cc_final: 0.9059 (m) REVERT: A 425 MET cc_start: 0.9192 (mmm) cc_final: 0.8879 (mmm) REVERT: B 384 TRP cc_start: 0.8350 (m100) cc_final: 0.7644 (m100) REVERT: B 425 MET cc_start: 0.8615 (tpp) cc_final: 0.7796 (mpp) REVERT: B 505 LEU cc_start: 0.8853 (tp) cc_final: 0.8291 (tp) REVERT: C 256 ASP cc_start: 0.7605 (p0) cc_final: 0.7198 (p0) REVERT: C 408 MET cc_start: 0.9238 (tpp) cc_final: 0.8452 (tpp) REVERT: C 412 VAL cc_start: 0.9331 (t) cc_final: 0.9055 (m) REVERT: C 425 MET cc_start: 0.9187 (mmm) cc_final: 0.8957 (mmm) outliers start: 2 outliers final: 0 residues processed: 323 average time/residue: 0.2407 time to fit residues: 121.1499 Evaluate side-chains 258 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 160 optimal weight: 3.9990 chunk 169 optimal weight: 0.2980 chunk 8 optimal weight: 0.0670 chunk 41 optimal weight: 0.0020 chunk 110 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 overall best weight: 0.3526 ------------------------------------------------------------------------------- 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 101 HIS ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112232 restraints weight = 30538.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115389 restraints weight = 18217.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117672 restraints weight = 12776.960| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16294 Z= 0.099 Angle : 0.561 8.498 22106 Z= 0.279 Chirality : 0.042 0.160 2452 Planarity : 0.003 0.039 2970 Dihedral : 3.547 15.458 2208 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 2026 helix: 1.26 (0.20), residues: 730 sheet: -0.12 (0.27), residues: 398 loop : -0.73 (0.23), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 384 HIS 0.002 0.000 HIS A 101 PHE 0.010 0.001 PHE A 283 TYR 0.010 0.001 TYR A 543 ARG 0.002 0.000 ARG B 497 Details of bonding type rmsd hydrogen bonds : bond 0.02561 ( 704) hydrogen bonds : angle 3.81292 ( 2184) covalent geometry : bond 0.00208 (16294) covalent geometry : angle 0.56132 (22106) *********************** 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 347 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8237 (m100) cc_final: 0.7552 (m100) REVERT: E 425 MET cc_start: 0.8566 (tpp) cc_final: 0.7713 (mpp) REVERT: E 505 LEU cc_start: 0.8903 (tp) cc_final: 0.8382 (tp) REVERT: A 256 ASP cc_start: 0.7598 (p0) cc_final: 0.7097 (p0) REVERT: A 408 MET cc_start: 0.9153 (tpp) cc_final: 0.8278 (tpp) REVERT: A 412 VAL cc_start: 0.9302 (t) cc_final: 0.9019 (m) REVERT: A 432 ASP cc_start: 0.8142 (m-30) cc_final: 0.7787 (m-30) REVERT: B 384 TRP cc_start: 0.8237 (m100) cc_final: 0.7548 (m100) REVERT: B 425 MET cc_start: 0.8556 (tpp) cc_final: 0.7707 (mpp) REVERT: B 505 LEU cc_start: 0.8904 (tp) cc_final: 0.8385 (tp) REVERT: C 256 ASP cc_start: 0.7609 (p0) cc_final: 0.7077 (p0) REVERT: C 408 MET cc_start: 0.9151 (tpp) cc_final: 0.8287 (tpp) REVERT: C 412 VAL cc_start: 0.9298 (t) cc_final: 0.9013 (m) REVERT: C 432 ASP cc_start: 0.8137 (m-30) cc_final: 0.7781 (m-30) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2537 time to fit residues: 135.7925 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 : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 53 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 271 GLN E 533 ASN A 101 HIS A 472 GLN B 271 GLN C 101 HIS C 472 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108177 restraints weight = 30719.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111207 restraints weight = 18611.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113351 restraints weight = 13153.965| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16294 Z= 0.215 Angle : 0.639 8.575 22106 Z= 0.323 Chirality : 0.045 0.159 2452 Planarity : 0.004 0.038 2970 Dihedral : 4.051 16.954 2208 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 2026 helix: 1.08 (0.20), residues: 732 sheet: -0.21 (0.27), residues: 396 loop : -0.86 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 487 HIS 0.004 0.001 HIS B 101 PHE 0.020 0.002 PHE E 296 TYR 0.015 0.002 TYR E 559 ARG 0.003 0.000 ARG B 497 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 704) hydrogen bonds : angle 4.25121 ( 2184) covalent geometry : bond 0.00482 (16294) covalent geometry : angle 0.63912 (22106) *********************** 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 319 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 90 ASP cc_start: 0.8105 (p0) cc_final: 0.7219 (t0) REVERT: E 384 TRP cc_start: 0.8440 (m100) cc_final: 0.7749 (m100) REVERT: E 492 GLU cc_start: 0.8243 (tp30) cc_final: 0.7931 (tp30) REVERT: E 505 LEU cc_start: 0.8712 (tp) cc_final: 0.8387 (tp) REVERT: A 256 ASP cc_start: 0.7661 (p0) cc_final: 0.7225 (p0) REVERT: A 400 ASP cc_start: 0.8445 (p0) cc_final: 0.7871 (t70) REVERT: A 408 MET cc_start: 0.9210 (tpp) cc_final: 0.8553 (tpp) REVERT: A 412 VAL cc_start: 0.9426 (t) cc_final: 0.9215 (m) REVERT: A 432 ASP cc_start: 0.7929 (m-30) cc_final: 0.7505 (m-30) REVERT: B 90 ASP cc_start: 0.8116 (p0) cc_final: 0.7224 (t0) REVERT: B 384 TRP cc_start: 0.8439 (m100) cc_final: 0.7748 (m100) REVERT: B 492 GLU cc_start: 0.8242 (tp30) cc_final: 0.7929 (tp30) REVERT: B 505 LEU cc_start: 0.8715 (tp) cc_final: 0.8388 (tp) REVERT: C 256 ASP cc_start: 0.7671 (p0) cc_final: 0.7266 (p0) REVERT: C 400 ASP cc_start: 0.8435 (p0) cc_final: 0.7870 (t70) REVERT: C 408 MET cc_start: 0.9208 (tpp) cc_final: 0.8554 (tpp) REVERT: C 412 VAL cc_start: 0.9424 (t) cc_final: 0.9211 (m) REVERT: C 432 ASP cc_start: 0.7931 (m-30) cc_final: 0.7506 (m-30) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2520 time to fit residues: 122.8222 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 : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 37 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.106615 restraints weight = 30911.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109755 restraints weight = 18442.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111982 restraints weight = 12962.805| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16294 Z= 0.115 Angle : 0.585 8.540 22106 Z= 0.292 Chirality : 0.043 0.169 2452 Planarity : 0.003 0.037 2970 Dihedral : 3.837 15.905 2208 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.66 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 2026 helix: 1.15 (0.20), residues: 730 sheet: -0.23 (0.27), residues: 402 loop : -0.79 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 384 HIS 0.003 0.000 HIS B 101 PHE 0.012 0.001 PHE A 283 TYR 0.020 0.002 TYR B 166 ARG 0.006 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.02866 ( 704) hydrogen bonds : angle 3.95404 ( 2184) covalent geometry : bond 0.00252 (16294) covalent geometry : angle 0.58504 (22106) *********************** 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 332 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 90 ASP cc_start: 0.8165 (p0) cc_final: 0.7226 (t0) REVERT: E 384 TRP cc_start: 0.8329 (m100) cc_final: 0.7614 (m100) REVERT: E 492 GLU cc_start: 0.8250 (tp30) cc_final: 0.7914 (tp30) REVERT: E 505 LEU cc_start: 0.8779 (tp) cc_final: 0.8436 (tp) REVERT: A 256 ASP cc_start: 0.7631 (p0) cc_final: 0.7117 (p0) REVERT: A 400 ASP cc_start: 0.8420 (p0) cc_final: 0.7831 (t70) REVERT: A 408 MET cc_start: 0.9183 (tpp) cc_final: 0.8394 (tpp) REVERT: A 412 VAL cc_start: 0.9367 (t) cc_final: 0.9131 (m) REVERT: A 432 ASP cc_start: 0.8284 (m-30) cc_final: 0.7906 (m-30) REVERT: A 492 GLU cc_start: 0.7336 (pm20) cc_final: 0.7065 (pm20) REVERT: B 90 ASP cc_start: 0.8161 (p0) cc_final: 0.7220 (t0) REVERT: B 384 TRP cc_start: 0.8332 (m100) cc_final: 0.7620 (m100) REVERT: B 425 MET cc_start: 0.8636 (tpp) cc_final: 0.7848 (tpp) REVERT: B 492 GLU cc_start: 0.8254 (tp30) cc_final: 0.7913 (tp30) REVERT: B 505 LEU cc_start: 0.8783 (tp) cc_final: 0.8432 (tp) REVERT: C 256 ASP cc_start: 0.7646 (p0) cc_final: 0.7121 (p0) REVERT: C 400 ASP cc_start: 0.8415 (p0) cc_final: 0.7825 (t70) REVERT: C 408 MET cc_start: 0.9180 (tpp) cc_final: 0.8394 (tpp) REVERT: C 412 VAL cc_start: 0.9366 (t) cc_final: 0.9127 (m) REVERT: C 432 ASP cc_start: 0.8282 (m-30) cc_final: 0.7903 (m-30) REVERT: C 492 GLU cc_start: 0.7339 (pm20) cc_final: 0.7069 (pm20) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2363 time to fit residues: 121.6727 Evaluate side-chains 263 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 168 optimal weight: 0.1980 chunk 133 optimal weight: 7.9990 chunk 196 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 153 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 45 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.137116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115445 restraints weight = 30305.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118627 restraints weight = 18457.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120710 restraints weight = 13017.624| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16294 Z= 0.107 Angle : 0.595 10.450 22106 Z= 0.291 Chirality : 0.042 0.171 2452 Planarity : 0.003 0.037 2970 Dihedral : 3.662 15.101 2208 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.66 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 2026 helix: 1.13 (0.20), residues: 732 sheet: -0.15 (0.27), residues: 398 loop : -0.80 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 347 HIS 0.003 0.000 HIS E 101 PHE 0.012 0.001 PHE C 283 TYR 0.019 0.002 TYR B 166 ARG 0.005 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.02685 ( 704) hydrogen bonds : angle 3.82583 ( 2184) covalent geometry : bond 0.00234 (16294) covalent geometry : angle 0.59498 (22106) *********************** 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 324 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 ASP cc_start: 0.8150 (p0) cc_final: 0.7126 (t0) REVERT: E 246 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7767 (mmtp) REVERT: E 425 MET cc_start: 0.8607 (tpp) cc_final: 0.7769 (tpp) REVERT: E 492 GLU cc_start: 0.8182 (tp30) cc_final: 0.7875 (tp30) REVERT: E 505 LEU cc_start: 0.8882 (tp) cc_final: 0.8507 (tp) REVERT: A 256 ASP cc_start: 0.7608 (p0) cc_final: 0.7073 (p0) REVERT: A 400 ASP cc_start: 0.8284 (p0) cc_final: 0.7636 (t70) REVERT: A 408 MET cc_start: 0.9155 (tpp) cc_final: 0.8359 (tpp) REVERT: A 412 VAL cc_start: 0.9349 (t) cc_final: 0.9118 (m) REVERT: A 432 ASP cc_start: 0.7665 (m-30) cc_final: 0.7287 (m-30) REVERT: A 492 GLU cc_start: 0.7414 (pm20) cc_final: 0.7160 (pm20) REVERT: B 90 ASP cc_start: 0.8148 (p0) cc_final: 0.7127 (t0) REVERT: B 246 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7775 (mmtp) REVERT: B 425 MET cc_start: 0.8582 (tpp) cc_final: 0.7760 (tpp) REVERT: B 492 GLU cc_start: 0.8189 (tp30) cc_final: 0.7882 (tp30) REVERT: B 505 LEU cc_start: 0.8886 (tp) cc_final: 0.8288 (tp) REVERT: C 256 ASP cc_start: 0.7507 (p0) cc_final: 0.6990 (p0) REVERT: C 400 ASP cc_start: 0.8282 (p0) cc_final: 0.7637 (t70) REVERT: C 408 MET cc_start: 0.9154 (tpp) cc_final: 0.8362 (tpp) REVERT: C 412 VAL cc_start: 0.9346 (t) cc_final: 0.9116 (m) REVERT: C 432 ASP cc_start: 0.7667 (m-30) cc_final: 0.7291 (m-30) REVERT: C 492 GLU cc_start: 0.7417 (pm20) cc_final: 0.7161 (pm20) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.2495 time to fit residues: 124.6169 Evaluate side-chains 265 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 74 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 81 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114593 restraints weight = 30630.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117742 restraints weight = 18590.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119930 restraints weight = 13107.274| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16294 Z= 0.111 Angle : 0.594 8.583 22106 Z= 0.293 Chirality : 0.043 0.176 2452 Planarity : 0.003 0.037 2970 Dihedral : 3.678 17.239 2208 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.29 % Rotamer: Outliers : 0.12 % Allowed : 0.12 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 2026 helix: 1.20 (0.20), residues: 732 sheet: -0.03 (0.28), residues: 390 loop : -0.84 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 487 HIS 0.002 0.000 HIS B 101 PHE 0.015 0.001 PHE C 74 TYR 0.019 0.002 TYR E 559 ARG 0.004 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.02721 ( 704) hydrogen bonds : angle 3.85191 ( 2184) covalent geometry : bond 0.00247 (16294) covalent geometry : angle 0.59445 (22106) ********************** 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 320 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 318 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 ASP cc_start: 0.8115 (p0) cc_final: 0.7126 (t0) REVERT: E 178 LEU cc_start: 0.7532 (tp) cc_final: 0.7331 (tt) REVERT: E 425 MET cc_start: 0.8585 (tpp) cc_final: 0.7785 (tpp) REVERT: E 492 GLU cc_start: 0.8198 (tp30) cc_final: 0.7883 (tp30) REVERT: E 505 LEU cc_start: 0.8796 (tp) cc_final: 0.8427 (tp) REVERT: A 218 ASP cc_start: 0.7969 (t70) cc_final: 0.7761 (t0) REVERT: A 256 ASP cc_start: 0.7609 (p0) cc_final: 0.7071 (p0) REVERT: A 400 ASP cc_start: 0.8292 (p0) cc_final: 0.7657 (t70) REVERT: A 408 MET cc_start: 0.9156 (tpp) cc_final: 0.8347 (tpp) REVERT: A 412 VAL cc_start: 0.9374 (t) cc_final: 0.9166 (m) REVERT: A 432 ASP cc_start: 0.7768 (m-30) cc_final: 0.7368 (m-30) REVERT: A 492 GLU cc_start: 0.7349 (pm20) cc_final: 0.6718 (pm20) REVERT: B 90 ASP cc_start: 0.8113 (p0) cc_final: 0.7131 (t0) REVERT: B 178 LEU cc_start: 0.7539 (tp) cc_final: 0.7335 (tt) REVERT: B 425 MET cc_start: 0.8569 (tpp) cc_final: 0.7746 (tpp) REVERT: B 492 GLU cc_start: 0.8205 (tp30) cc_final: 0.7892 (tp30) REVERT: B 505 LEU cc_start: 0.8800 (tp) cc_final: 0.8427 (tp) REVERT: C 218 ASP cc_start: 0.7971 (t70) cc_final: 0.7769 (t0) REVERT: C 256 ASP cc_start: 0.7538 (p0) cc_final: 0.7006 (p0) REVERT: C 400 ASP cc_start: 0.8290 (p0) cc_final: 0.7655 (t70) REVERT: C 408 MET cc_start: 0.9155 (tpp) cc_final: 0.8349 (tpp) REVERT: C 412 VAL cc_start: 0.9374 (t) cc_final: 0.9164 (m) REVERT: C 432 ASP cc_start: 0.7759 (m-30) cc_final: 0.7357 (m-30) REVERT: C 492 GLU cc_start: 0.7363 (pm20) cc_final: 0.6730 (pm20) outliers start: 2 outliers final: 0 residues processed: 318 average time/residue: 0.2666 time to fit residues: 132.5907 Evaluate side-chains 267 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 122 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115230 restraints weight = 30478.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118415 restraints weight = 18518.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120598 restraints weight = 13020.630| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2018 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= 0.106 Angle : 0.589 8.764 22106 Z= 0.288 Chirality : 0.042 0.172 2452 Planarity : 0.003 0.037 2970 Dihedral : 3.573 14.784 2208 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.76 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 2026 helix: 1.23 (0.20), residues: 732 sheet: -0.23 (0.27), residues: 390 loop : -0.80 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 384 HIS 0.002 0.000 HIS E 101 PHE 0.014 0.001 PHE A 283 TYR 0.021 0.001 TYR E 559 ARG 0.004 0.000 ARG B 333 Details of bonding type rmsd hydrogen bonds : bond 0.02620 ( 704) hydrogen bonds : angle 3.77243 ( 2184) covalent geometry : bond 0.00234 (16294) covalent geometry : angle 0.58863 (22106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4711.53 seconds wall clock time: 82 minutes 33.89 seconds (4953.89 seconds total)