Starting phenix.real_space_refine on Sat May 17 15:31:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8igg_35432/05_2025/8igg_35432.cif Found real_map, /net/cci-nas-00/data/ceres_data/8igg_35432/05_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_35432/05_2025/8igg_35432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8igg_35432/05_2025/8igg_35432.map" model { file = "/net/cci-nas-00/data/ceres_data/8igg_35432/05_2025/8igg_35432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8igg_35432/05_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-5687/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: 12.64, per 1000 atoms: 0.79 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: 3.44 Conformation dependent library (CDL) restraints added in 1.9 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: 2.18 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: 5.22 Time building geometry restraints manager: 4.10 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: 0.530 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.810 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.120 ------------------------------------------------------------------------------- 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 : 1.848 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: 0.2393 time to fit residues: 130.9961 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 : 1.764 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109589 restraints weight = 30858.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112635 restraints weight = 18833.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114728 restraints weight = 13393.304| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 1.526 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: 0.9513 (mp) cc_final: 0.9312 (mt) REVERT: E 295 MET cc_start: 0.7995 (ptt) cc_final: 0.7751 (ptt) REVERT: E 384 TRP cc_start: 0.8349 (m100) cc_final: 0.7655 (m100) REVERT: E 505 LEU cc_start: 0.8870 (tp) cc_final: 0.8531 (tp) REVERT: A 256 ASP cc_start: 0.7687 (p0) cc_final: 0.7331 (p0) REVERT: A 408 MET cc_start: 0.9089 (tpp) cc_final: 0.8280 (tpp) REVERT: A 432 ASP cc_start: 0.7958 (m-30) cc_final: 0.7512 (m-30) REVERT: B 295 MET cc_start: 0.7989 (ptt) cc_final: 0.7749 (ptt) REVERT: B 384 TRP cc_start: 0.8349 (m100) cc_final: 0.7653 (m100) REVERT: B 505 LEU cc_start: 0.8874 (tp) cc_final: 0.8534 (tp) REVERT: C 256 ASP cc_start: 0.7684 (p0) cc_final: 0.7330 (p0) REVERT: C 408 MET cc_start: 0.9088 (tpp) cc_final: 0.8282 (tpp) REVERT: C 432 ASP cc_start: 0.7949 (m-30) cc_final: 0.7507 (m-30) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.2502 time to fit residues: 124.3365 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 : 1.692 ------------------------------------------------------------------------------- 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: 0.3980 chunk 157 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 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: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 533 ASN A 279 GLN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3544 r_free = 0.3544 target = 0.131106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109200 restraints weight = 30499.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112167 restraints weight = 18604.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114289 restraints weight = 13293.780| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16294 Z= 0.133 Angle : 0.564 8.706 22106 Z= 0.282 Chirality : 0.043 0.162 2452 Planarity : 0.004 0.043 2970 Dihedral : 3.844 13.468 2208 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.16 % Favored : 92.74 % Rotamer: Outliers : 0.06 % Allowed : 4.91 % Favored : 95.04 % 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: 1.10 (0.20), residues: 732 sheet: -0.36 (0.27), residues: 400 loop : -0.77 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 487 HIS 0.002 0.001 HIS E 101 PHE 0.011 0.001 PHE C 167 TYR 0.020 0.001 TYR C 570 ARG 0.004 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 704) hydrogen bonds : angle 4.17698 ( 2184) covalent geometry : bond 0.00296 (16294) covalent geometry : angle 0.56412 (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 344 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8329 (m100) cc_final: 0.7609 (m100) REVERT: E 505 LEU cc_start: 0.8813 (tp) cc_final: 0.8355 (tp) REVERT: A 215 ASN cc_start: 0.8327 (t0) cc_final: 0.8124 (t0) REVERT: A 218 ASP cc_start: 0.7847 (t70) cc_final: 0.7493 (t0) REVERT: A 256 ASP cc_start: 0.7680 (p0) cc_final: 0.7288 (p0) REVERT: A 408 MET cc_start: 0.9204 (tpp) cc_final: 0.8204 (tpp) REVERT: A 412 VAL cc_start: 0.9280 (t) cc_final: 0.9013 (m) REVERT: A 432 ASP cc_start: 0.8039 (m-30) cc_final: 0.7737 (m-30) REVERT: A 492 GLU cc_start: 0.7472 (pm20) cc_final: 0.6582 (pm20) REVERT: B 384 TRP cc_start: 0.8336 (m100) cc_final: 0.7610 (m100) REVERT: B 505 LEU cc_start: 0.8811 (tp) cc_final: 0.8353 (tp) REVERT: C 215 ASN cc_start: 0.8336 (t0) cc_final: 0.8131 (t0) REVERT: C 218 ASP cc_start: 0.7851 (t70) cc_final: 0.7497 (t0) REVERT: C 256 ASP cc_start: 0.7678 (p0) cc_final: 0.7282 (p0) REVERT: C 408 MET cc_start: 0.9200 (tpp) cc_final: 0.8206 (tpp) REVERT: C 412 VAL cc_start: 0.9276 (t) cc_final: 0.9011 (m) REVERT: C 432 ASP cc_start: 0.8031 (m-30) cc_final: 0.7735 (m-30) REVERT: C 492 GLU cc_start: 0.7477 (pm20) cc_final: 0.6585 (pm20) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.2433 time to fit residues: 128.2047 Evaluate side-chains 264 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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: 6.9990 chunk 113 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110316 restraints weight = 30232.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113403 restraints weight = 18218.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115554 restraints weight = 12748.355| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16294 Z= 0.155 Angle : 0.579 8.570 22106 Z= 0.290 Chirality : 0.043 0.176 2452 Planarity : 0.004 0.043 2970 Dihedral : 3.907 13.915 2208 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % 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: -0.11 (0.20), residues: 2026 helix: 1.04 (0.20), residues: 732 sheet: -0.38 (0.26), residues: 402 loop : -0.80 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.003 0.001 HIS E 101 PHE 0.013 0.001 PHE E 296 TYR 0.010 0.001 TYR A 543 ARG 0.004 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 704) hydrogen bonds : angle 4.24510 ( 2184) covalent geometry : bond 0.00346 (16294) covalent geometry : angle 0.57943 (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 329 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8355 (m100) cc_final: 0.7660 (m100) REVERT: E 505 LEU cc_start: 0.8741 (tp) cc_final: 0.8420 (tp) REVERT: A 256 ASP cc_start: 0.7645 (p0) cc_final: 0.7253 (p0) REVERT: A 408 MET cc_start: 0.9269 (tpp) cc_final: 0.8554 (tpp) REVERT: A 412 VAL cc_start: 0.9335 (t) cc_final: 0.9081 (m) REVERT: A 432 ASP cc_start: 0.8066 (m-30) cc_final: 0.7769 (m-30) REVERT: A 492 GLU cc_start: 0.7539 (pm20) cc_final: 0.6508 (pm20) REVERT: B 384 TRP cc_start: 0.8361 (m100) cc_final: 0.7660 (m100) REVERT: B 505 LEU cc_start: 0.8744 (tp) cc_final: 0.8421 (tp) REVERT: C 256 ASP cc_start: 0.7646 (p0) cc_final: 0.7252 (p0) REVERT: C 408 MET cc_start: 0.9267 (tpp) cc_final: 0.8561 (tpp) REVERT: C 412 VAL cc_start: 0.9329 (t) cc_final: 0.9074 (m) REVERT: C 432 ASP cc_start: 0.8061 (m-30) cc_final: 0.7765 (m-30) REVERT: C 492 GLU cc_start: 0.7542 (pm20) cc_final: 0.6508 (pm20) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.2369 time to fit residues: 120.2162 Evaluate side-chains 268 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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: 0.4980 chunk 129 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 40 optimal weight: 0.0030 chunk 109 optimal weight: 7.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111919 restraints weight = 30687.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115099 restraints weight = 18215.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117331 restraints weight = 12636.759| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16294 Z= 0.120 Angle : 0.562 8.336 22106 Z= 0.281 Chirality : 0.042 0.173 2452 Planarity : 0.003 0.042 2970 Dihedral : 3.821 15.075 2208 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % 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: -0.06 (0.20), residues: 2026 helix: 1.08 (0.20), residues: 732 sheet: -0.40 (0.26), residues: 406 loop : -0.74 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 105 HIS 0.002 0.000 HIS B 101 PHE 0.012 0.001 PHE C 283 TYR 0.015 0.001 TYR C 543 ARG 0.003 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.02933 ( 704) hydrogen bonds : angle 4.04789 ( 2184) covalent geometry : bond 0.00266 (16294) covalent geometry : angle 0.56233 (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 332 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 314 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7702 (tp40) REVERT: E 384 TRP cc_start: 0.8334 (m100) cc_final: 0.7650 (m100) REVERT: E 505 LEU cc_start: 0.8729 (tp) cc_final: 0.8399 (tp) REVERT: A 256 ASP cc_start: 0.7611 (p0) cc_final: 0.7199 (p0) REVERT: A 408 MET cc_start: 0.9232 (tpp) cc_final: 0.8435 (tpp) REVERT: A 412 VAL cc_start: 0.9331 (t) cc_final: 0.9067 (m) REVERT: A 432 ASP cc_start: 0.7803 (m-30) cc_final: 0.7351 (m-30) REVERT: A 492 GLU cc_start: 0.7605 (pm20) cc_final: 0.6612 (pm20) REVERT: B 314 GLN cc_start: 0.7961 (tp-100) cc_final: 0.7712 (tp40) REVERT: B 384 TRP cc_start: 0.8339 (m100) cc_final: 0.7651 (m100) REVERT: B 505 LEU cc_start: 0.8802 (tp) cc_final: 0.8462 (tp) REVERT: C 256 ASP cc_start: 0.7600 (p0) cc_final: 0.7187 (p0) REVERT: C 408 MET cc_start: 0.9226 (tpp) cc_final: 0.8434 (tpp) REVERT: C 412 VAL cc_start: 0.9329 (t) cc_final: 0.9062 (m) REVERT: C 432 ASP cc_start: 0.7807 (m-30) cc_final: 0.7355 (m-30) REVERT: C 492 GLU cc_start: 0.7611 (pm20) cc_final: 0.6616 (pm20) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2385 time to fit residues: 122.5193 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 : 1.819 ------------------------------------------------------------------------------- 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: 0.0000 chunk 169 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 110 optimal weight: 0.0370 chunk 139 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 overall best weight: 0.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** 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 = 0.3618 r_free = 0.3618 target = 0.136924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115430 restraints weight = 30460.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118597 restraints weight = 18384.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120868 restraints weight = 12899.054| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16294 Z= 0.099 Angle : 0.562 8.330 22106 Z= 0.276 Chirality : 0.042 0.175 2452 Planarity : 0.003 0.043 2970 Dihedral : 3.654 15.444 2208 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 1.16 (0.20), residues: 730 sheet: -0.14 (0.27), residues: 394 loop : -0.75 (0.23), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 384 HIS 0.002 0.000 HIS E 101 PHE 0.011 0.001 PHE A 74 TYR 0.010 0.001 TYR A 543 ARG 0.002 0.000 ARG B 497 Details of bonding type rmsd hydrogen bonds : bond 0.02678 ( 704) hydrogen bonds : angle 3.88741 ( 2184) covalent geometry : bond 0.00212 (16294) covalent geometry : angle 0.56193 (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 355 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 314 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7667 (tp40) REVERT: E 425 MET cc_start: 0.8635 (tpp) cc_final: 0.7815 (mpp) REVERT: E 505 LEU cc_start: 0.8866 (tp) cc_final: 0.8248 (tp) REVERT: A 256 ASP cc_start: 0.7570 (p0) cc_final: 0.7104 (p0) REVERT: A 260 ASN cc_start: 0.8278 (m-40) cc_final: 0.8070 (m-40) REVERT: A 408 MET cc_start: 0.9170 (tpp) cc_final: 0.8318 (tpp) REVERT: A 412 VAL cc_start: 0.9315 (t) cc_final: 0.9054 (m) REVERT: A 432 ASP cc_start: 0.7861 (m-30) cc_final: 0.7566 (m-30) REVERT: A 492 GLU cc_start: 0.7642 (pm20) cc_final: 0.6719 (pm20) REVERT: B 314 GLN cc_start: 0.7901 (tp-100) cc_final: 0.7677 (tp40) REVERT: B 425 MET cc_start: 0.8640 (tpp) cc_final: 0.7821 (mpp) REVERT: B 505 LEU cc_start: 0.8869 (tp) cc_final: 0.8246 (tp) REVERT: C 256 ASP cc_start: 0.7572 (p0) cc_final: 0.7108 (p0) REVERT: C 260 ASN cc_start: 0.8279 (m-40) cc_final: 0.8074 (m-40) REVERT: C 408 MET cc_start: 0.9169 (tpp) cc_final: 0.8318 (tpp) REVERT: C 412 VAL cc_start: 0.9312 (t) cc_final: 0.9048 (m) REVERT: C 432 ASP cc_start: 0.7855 (m-30) cc_final: 0.7564 (m-30) REVERT: C 492 GLU cc_start: 0.7651 (pm20) cc_final: 0.6724 (pm20) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2519 time to fit residues: 136.6768 Evaluate side-chains 281 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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: 10.0000 chunk 155 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 271 GLN A 101 HIS A 117 ASN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN C 101 HIS C 117 ASN C 472 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107986 restraints weight = 30956.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111043 restraints weight = 18598.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113158 restraints weight = 13026.862| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16294 Z= 0.193 Angle : 0.627 8.544 22106 Z= 0.317 Chirality : 0.044 0.153 2452 Planarity : 0.004 0.042 2970 Dihedral : 4.020 16.982 2208 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.85 % Favored : 92.05 % Rotamer: Outliers : 0.12 % Allowed : 1.65 % Favored : 98.23 % 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: -0.08 (0.20), residues: 2026 helix: 1.02 (0.20), residues: 732 sheet: -0.06 (0.27), residues: 370 loop : -0.89 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 487 HIS 0.003 0.001 HIS B 101 PHE 0.018 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 0.03298 ( 704) hydrogen bonds : angle 4.23692 ( 2184) covalent geometry : bond 0.00435 (16294) covalent geometry : angle 0.62655 (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 337 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 335 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 TRP cc_start: 0.8429 (m100) cc_final: 0.7721 (m100) REVERT: E 505 LEU cc_start: 0.8741 (tp) cc_final: 0.8390 (tp) REVERT: A 256 ASP cc_start: 0.7661 (p0) cc_final: 0.7275 (p0) REVERT: A 408 MET cc_start: 0.9238 (tpp) cc_final: 0.8492 (tpp) REVERT: A 412 VAL cc_start: 0.9406 (t) cc_final: 0.9178 (m) REVERT: A 425 MET cc_start: 0.9147 (mmm) cc_final: 0.8833 (mmm) REVERT: A 432 ASP cc_start: 0.7952 (m-30) cc_final: 0.7671 (m-30) REVERT: B 314 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7903 (tp40) REVERT: B 384 TRP cc_start: 0.8431 (m100) cc_final: 0.7722 (m100) REVERT: B 505 LEU cc_start: 0.8740 (tp) cc_final: 0.8392 (tp) REVERT: C 256 ASP cc_start: 0.7657 (p0) cc_final: 0.7268 (p0) REVERT: C 408 MET cc_start: 0.9234 (tpp) cc_final: 0.8492 (tpp) REVERT: C 412 VAL cc_start: 0.9403 (t) cc_final: 0.9176 (m) REVERT: C 425 MET cc_start: 0.9136 (mmm) cc_final: 0.8818 (mmm) REVERT: C 432 ASP cc_start: 0.7956 (m-30) cc_final: 0.7669 (m-30) outliers start: 2 outliers final: 0 residues processed: 337 average time/residue: 0.2604 time to fit residues: 136.7428 Evaluate side-chains 279 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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: 1.9990 chunk 48 optimal weight: 0.0050 chunk 64 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 131 optimal weight: 0.0070 overall best weight: 0.5012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114435 restraints weight = 30565.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117612 restraints weight = 18465.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119829 restraints weight = 13031.001| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16294 Z= 0.106 Angle : 0.589 8.550 22106 Z= 0.291 Chirality : 0.043 0.164 2452 Planarity : 0.003 0.043 2970 Dihedral : 3.771 15.569 2208 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.71 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 0.04 (0.20), residues: 2026 helix: 1.15 (0.20), residues: 732 sheet: -0.14 (0.27), residues: 398 loop : -0.78 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 487 HIS 0.002 0.000 HIS E 101 PHE 0.011 0.001 PHE C 283 TYR 0.016 0.002 TYR B 166 ARG 0.005 0.000 ARG E 497 Details of bonding type rmsd hydrogen bonds : bond 0.02716 ( 704) hydrogen bonds : angle 3.89287 ( 2184) covalent geometry : bond 0.00223 (16294) covalent geometry : angle 0.58854 (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 339 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7763 (mmtp) REVERT: E 384 TRP cc_start: 0.8266 (m100) cc_final: 0.7567 (m100) REVERT: E 505 LEU cc_start: 0.8829 (tp) cc_final: 0.8445 (tp) REVERT: A 256 ASP cc_start: 0.7601 (p0) cc_final: 0.7157 (p0) REVERT: A 408 MET cc_start: 0.9152 (tpp) cc_final: 0.8312 (tpp) REVERT: A 412 VAL cc_start: 0.9335 (t) cc_final: 0.9072 (m) REVERT: A 425 MET cc_start: 0.9111 (mmm) cc_final: 0.8806 (mmm) REVERT: A 432 ASP cc_start: 0.8180 (m-30) cc_final: 0.7843 (m-30) REVERT: B 246 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7764 (mmtp) REVERT: B 505 LEU cc_start: 0.8833 (tp) cc_final: 0.8460 (tp) REVERT: C 256 ASP cc_start: 0.7589 (p0) cc_final: 0.7144 (p0) REVERT: C 408 MET cc_start: 0.9150 (tpp) cc_final: 0.8310 (tpp) REVERT: C 412 VAL cc_start: 0.9331 (t) cc_final: 0.9067 (m) REVERT: C 425 MET cc_start: 0.9105 (mmm) cc_final: 0.8803 (mmm) REVERT: C 432 ASP cc_start: 0.8179 (m-30) cc_final: 0.7838 (m-30) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2272 time to fit residues: 119.1949 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 : 1.731 ------------------------------------------------------------------------------- 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: 3.9990 chunk 133 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114212 restraints weight = 30228.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117404 restraints weight = 18013.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119640 restraints weight = 12532.447| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1854 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= 0.112 Angle : 0.585 8.482 22106 Z= 0.292 Chirality : 0.043 0.163 2452 Planarity : 0.003 0.043 2970 Dihedral : 3.750 17.631 2208 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.81 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.19 (0.20), residues: 732 sheet: -0.11 (0.27), residues: 394 loop : -0.83 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 487 HIS 0.002 0.000 HIS E 101 PHE 0.012 0.001 PHE C 74 TYR 0.018 0.002 TYR E 559 ARG 0.002 0.000 ARG B 497 Details of bonding type rmsd hydrogen bonds : bond 0.02793 ( 704) hydrogen bonds : angle 3.88485 ( 2184) covalent geometry : bond 0.00244 (16294) covalent geometry : angle 0.58539 (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 326 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 ASP cc_start: 0.8145 (p0) cc_final: 0.7142 (t0) REVERT: E 246 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7847 (mmtp) REVERT: E 384 TRP cc_start: 0.8296 (m100) cc_final: 0.7628 (m100) REVERT: E 425 MET cc_start: 0.8668 (tpp) cc_final: 0.7867 (mpp) REVERT: E 505 LEU cc_start: 0.8810 (tp) cc_final: 0.8427 (tp) REVERT: A 256 ASP cc_start: 0.7601 (p0) cc_final: 0.7157 (p0) REVERT: A 408 MET cc_start: 0.9185 (tpp) cc_final: 0.8354 (tpp) REVERT: A 412 VAL cc_start: 0.9356 (t) cc_final: 0.9142 (m) REVERT: A 432 ASP cc_start: 0.8160 (m-30) cc_final: 0.7810 (m-30) REVERT: B 90 ASP cc_start: 0.8156 (p0) cc_final: 0.7159 (t0) REVERT: B 246 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7854 (mmtp) REVERT: B 347 TRP cc_start: 0.9087 (m100) cc_final: 0.8884 (m100) REVERT: B 384 TRP cc_start: 0.8292 (m100) cc_final: 0.7627 (m100) REVERT: B 425 MET cc_start: 0.8679 (tpp) cc_final: 0.7886 (mpp) REVERT: B 505 LEU cc_start: 0.8816 (tp) cc_final: 0.8431 (tp) REVERT: C 256 ASP cc_start: 0.7591 (p0) cc_final: 0.7149 (p0) REVERT: C 408 MET cc_start: 0.9177 (tpp) cc_final: 0.8357 (tpp) REVERT: C 412 VAL cc_start: 0.9350 (t) cc_final: 0.9136 (m) REVERT: C 432 ASP cc_start: 0.8154 (m-30) cc_final: 0.7804 (m-30) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2340 time to fit residues: 118.5873 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 : 1.739 ------------------------------------------------------------------------------- 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: 4.9990 chunk 78 optimal weight: 0.0050 chunk 189 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 122 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.137042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115869 restraints weight = 30372.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119089 restraints weight = 18073.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121326 restraints weight = 12550.590| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16294 Z= 0.105 Angle : 0.587 8.706 22106 Z= 0.290 Chirality : 0.042 0.167 2452 Planarity : 0.003 0.043 2970 Dihedral : 3.652 14.913 2208 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.66 % Favored : 93.24 % 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: 0.04 (0.20), residues: 2026 helix: 1.21 (0.20), residues: 732 sheet: -0.12 (0.27), residues: 398 loop : -0.86 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 487 HIS 0.002 0.000 HIS E 101 PHE 0.011 0.001 PHE C 283 TYR 0.019 0.002 TYR E 559 ARG 0.006 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.02674 ( 704) hydrogen bonds : angle 3.78436 ( 2184) covalent geometry : bond 0.00228 (16294) covalent geometry : angle 0.58696 (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 340 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 ASP cc_start: 0.8126 (p0) cc_final: 0.7083 (t0) REVERT: E 384 TRP cc_start: 0.8263 (m100) cc_final: 0.7620 (m100) REVERT: E 425 MET cc_start: 0.8634 (tpp) cc_final: 0.7780 (mpp) REVERT: E 505 LEU cc_start: 0.8836 (tp) cc_final: 0.8444 (tp) REVERT: A 218 ASP cc_start: 0.7984 (t70) cc_final: 0.7747 (t0) REVERT: A 256 ASP cc_start: 0.7587 (p0) cc_final: 0.7098 (p0) REVERT: A 408 MET cc_start: 0.9121 (tpp) cc_final: 0.8228 (tpp) REVERT: A 412 VAL cc_start: 0.9347 (t) cc_final: 0.9140 (m) REVERT: A 425 MET cc_start: 0.9092 (mmm) cc_final: 0.8839 (mmm) REVERT: A 432 ASP cc_start: 0.8158 (m-30) cc_final: 0.7790 (m-30) REVERT: B 90 ASP cc_start: 0.8141 (p0) cc_final: 0.7094 (t0) REVERT: B 425 MET cc_start: 0.8645 (tpp) cc_final: 0.7808 (mpp) REVERT: B 505 LEU cc_start: 0.8840 (tp) cc_final: 0.8452 (tp) REVERT: C 218 ASP cc_start: 0.7981 (t70) cc_final: 0.7746 (t0) REVERT: C 256 ASP cc_start: 0.7584 (p0) cc_final: 0.7101 (p0) REVERT: C 408 MET cc_start: 0.9119 (tpp) cc_final: 0.8223 (tpp) REVERT: C 412 VAL cc_start: 0.9341 (t) cc_final: 0.9135 (m) REVERT: C 425 MET cc_start: 0.9076 (mmm) cc_final: 0.8822 (mmm) REVERT: C 432 ASP cc_start: 0.8154 (m-30) cc_final: 0.7779 (m-30) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.2739 time to fit residues: 142.6236 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 : 1.687 ------------------------------------------------------------------------------- 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: 0.6980 chunk 30 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 193 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 472 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114837 restraints weight = 30581.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117995 restraints weight = 18663.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120128 restraints weight = 13164.363| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16294 Z= 0.110 Angle : 0.582 8.526 22106 Z= 0.291 Chirality : 0.043 0.166 2452 Planarity : 0.004 0.043 2970 Dihedral : 3.633 14.571 2208 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.26 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 0.04 (0.20), residues: 2026 helix: 1.24 (0.20), residues: 732 sheet: -0.17 (0.28), residues: 380 loop : -0.84 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 487 HIS 0.002 0.000 HIS E 101 PHE 0.014 0.001 PHE C 74 TYR 0.021 0.002 TYR E 559 ARG 0.002 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.02716 ( 704) hydrogen bonds : angle 3.80669 ( 2184) covalent geometry : bond 0.00240 (16294) covalent geometry : angle 0.58189 (22106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4340.71 seconds wall clock time: 76 minutes 56.31 seconds (4616.31 seconds total)