Starting phenix.real_space_refine on Mon May 4 00:37:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20yw_67421/05_2026/20yw_67421.cif Found real_map, /net/cci-nas-00/data/ceres_data/20yw_67421/05_2026/20yw_67421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/20yw_67421/05_2026/20yw_67421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20yw_67421/05_2026/20yw_67421.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/20yw_67421/05_2026/20yw_67421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20yw_67421/05_2026/20yw_67421.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 44 5.16 5 C 10601 2.51 5 N 2790 2.21 5 O 3139 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16574 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4792 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 569} Chain breaks: 3 Chain: "B" Number of atoms: 4792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4792 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 569} Chain breaks: 3 Chain: "C" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3491 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 411} Chain breaks: 1 Chain: "D" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3499 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 412} Chain breaks: 2 Time building chain proxies: 4.08, per 1000 atoms: 0.25 Number of scatterers: 16574 At special positions: 0 Unit cell: (118.845, 122.265, 132.525, 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 44 16.00 O 3139 8.00 N 2790 7.00 C 10601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 82 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 273 " distance=2.04 Simple disulfide: pdb=" SG CYS C 82 " - pdb=" SG CYS C 273 " distance=2.04 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 273 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 756.1 milliseconds 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 12 sheets defined 65.0% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 70 through 89 removed outlier: 3.928A pdb=" N ILE A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 159 removed outlier: 3.594A pdb=" N LEU A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 181 removed outlier: 3.647A pdb=" N LYS A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.721A pdb=" N GLN A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 removed outlier: 3.557A pdb=" N ASN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 302 through 311 removed outlier: 3.841A pdb=" N GLN A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 327 through 346 removed outlier: 4.009A pdb=" N GLU A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 380 through 388 removed outlier: 3.523A pdb=" N ILE A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 412 Processing helix chain 'A' and resid 414 through 435 removed outlier: 3.621A pdb=" N LYS A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 456 removed outlier: 3.509A pdb=" N GLN A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 479 Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.955A pdb=" N PHE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 516 through 530 removed outlier: 4.051A pdb=" N GLU A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 533 No H-bonds generated for 'chain 'A' and resid 531 through 533' Processing helix chain 'A' and resid 534 through 557 removed outlier: 3.590A pdb=" N ILE A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 553 " --> pdb=" O ILE A 549 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 576 removed outlier: 4.485A pdb=" N SER A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 615 removed outlier: 3.738A pdb=" N LEU A 604 " --> pdb=" O ASN A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.794A pdb=" N TRP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 649 removed outlier: 4.384A pdb=" N ALA A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 38 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 70 through 88 Processing helix chain 'B' and resid 130 through 159 removed outlier: 3.597A pdb=" N LEU B 134 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 183 removed outlier: 3.833A pdb=" N THR B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 219 through 234 removed outlier: 4.171A pdb=" N GLU B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 271 removed outlier: 3.584A pdb=" N TYR B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Proline residue: B 257 - end of helix removed outlier: 3.764A pdb=" N ASN B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 302 removed outlier: 3.511A pdb=" N ILE B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.728A pdb=" N GLN B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 327 through 346 removed outlier: 4.174A pdb=" N GLU B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 removed outlier: 4.449A pdb=" N GLU B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 388 Proline residue: B 382 - end of helix removed outlier: 3.557A pdb=" N GLU B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 412 removed outlier: 3.972A pdb=" N GLN B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 435 removed outlier: 3.587A pdb=" N GLU B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 458 through 479 removed outlier: 3.683A pdb=" N TYR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 511 removed outlier: 3.529A pdb=" N CYS B 504 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 508 " --> pdb=" O CYS B 504 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 516 through 530 removed outlier: 3.548A pdb=" N GLU B 526 " --> pdb=" O ARG B 522 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 533 No H-bonds generated for 'chain 'B' and resid 531 through 533' Processing helix chain 'B' and resid 534 through 558 removed outlier: 3.648A pdb=" N LYS B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 576 removed outlier: 3.925A pdb=" N HIS B 569 " --> pdb=" O ASN B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 615 Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.728A pdb=" N ILE B 631 " --> pdb=" O ALA B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.815A pdb=" N ALA B 648 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 38 Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 70 through 88 removed outlier: 3.570A pdb=" N ILE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 159 removed outlier: 3.654A pdb=" N LEU C 134 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 181 Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.631A pdb=" N ALA C 215 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 234 removed outlier: 3.765A pdb=" N GLU C 234 " --> pdb=" O LYS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 272 removed outlier: 3.766A pdb=" N TYR C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Proline residue: C 257 - end of helix Processing helix chain 'C' and resid 295 through 302 Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.945A pdb=" N GLN C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 325 Processing helix chain 'C' and resid 327 through 346 removed outlier: 4.349A pdb=" N GLU C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 368 removed outlier: 4.302A pdb=" N GLU C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 388 Proline residue: C 382 - end of helix removed outlier: 3.595A pdb=" N GLU C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 396 Processing helix chain 'C' and resid 396 through 413 removed outlier: 4.128A pdb=" N GLN C 400 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR C 412 " --> pdb=" O TYR C 408 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 434 Processing helix chain 'C' and resid 441 through 455 Processing helix chain 'C' and resid 458 through 476 removed outlier: 3.559A pdb=" N GLN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 38 Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 70 through 89 removed outlier: 4.071A pdb=" N ILE D 89 " --> pdb=" O PHE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 158 removed outlier: 3.503A pdb=" N LYS D 154 " --> pdb=" O ILE D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 181 removed outlier: 3.643A pdb=" N LYS D 181 " --> pdb=" O GLY D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 233 Processing helix chain 'D' and resid 247 through 250 removed outlier: 4.167A pdb=" N GLU D 250 " --> pdb=" O SER D 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 247 through 250' Processing helix chain 'D' and resid 251 through 271 removed outlier: 3.783A pdb=" N TYR D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Proline residue: D 257 - end of helix removed outlier: 3.793A pdb=" N ASN D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 302 Processing helix chain 'D' and resid 302 through 311 removed outlier: 3.936A pdb=" N GLN D 306 " --> pdb=" O ASN D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 325 Processing helix chain 'D' and resid 327 through 346 removed outlier: 4.220A pdb=" N GLU D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 368 removed outlier: 4.190A pdb=" N GLU D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 388 Proline residue: D 382 - end of helix removed outlier: 3.780A pdb=" N ALA D 387 " --> pdb=" O LYS D 383 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 395 removed outlier: 3.542A pdb=" N ARG D 395 " --> pdb=" O GLY D 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 392 through 395' Processing helix chain 'D' and resid 396 through 413 removed outlier: 3.891A pdb=" N TYR D 408 " --> pdb=" O ALA D 404 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 409 " --> pdb=" O ILE D 405 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 434 removed outlier: 3.533A pdb=" N GLN D 419 " --> pdb=" O SER D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 456 removed outlier: 3.907A pdb=" N LEU D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 46 removed outlier: 6.320A pdb=" N THR A 96 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N THR A 350 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU A 98 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 12.313A pdb=" N VAL A 352 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N THR A 100 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 11.818A pdb=" N ALA A 354 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N ILE A 102 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE A 104 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE A 127 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY A 57 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE A 127 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR A 59 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ASP A 129 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ILE A 201 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 58 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 186 Processing sheet with id=AA3, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 46 removed outlier: 6.440A pdb=" N THR B 96 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THR B 350 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N LEU B 98 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 12.454A pdb=" N VAL B 352 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N THR B 100 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 11.979A pdb=" N ALA B 354 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N ILE B 102 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE B 104 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE B 127 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY B 57 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE B 127 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TYR B 59 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ASP B 129 " --> pdb=" O TYR B 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 184 through 186 Processing sheet with id=AA6, first strand: chain 'B' and resid 206 through 207 Processing sheet with id=AA7, first strand: chain 'C' and resid 40 through 46 removed outlier: 6.299A pdb=" N THR C 96 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N THR C 350 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N LEU C 98 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 12.417A pdb=" N VAL C 352 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N THR C 100 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N ALA C 354 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N ILE C 102 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE C 104 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE C 127 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 57 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE C 127 " --> pdb=" O GLY C 57 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR C 59 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASP C 129 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N ILE C 201 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU C 58 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 186 Processing sheet with id=AA9, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AB1, first strand: chain 'D' and resid 40 through 46 removed outlier: 6.360A pdb=" N THR D 96 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR D 350 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LEU D 98 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 12.427A pdb=" N VAL D 352 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N THR D 100 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 11.929A pdb=" N ALA D 354 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N ILE D 102 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE D 102 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY D 57 " --> pdb=" O MET D 125 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE D 127 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR D 59 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ASP D 129 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ILE D 201 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU D 58 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 184 through 186 Processing sheet with id=AB3, first strand: chain 'D' and resid 206 through 207 899 hydrogen bonds defined for protein. 2661 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2794 1.31 - 1.44: 4378 1.44 - 1.57: 9651 1.57 - 1.69: 0 1.69 - 1.82: 70 Bond restraints: 16893 Sorted by residual: bond pdb=" C LEU B 374 " pdb=" O LEU B 374 " ideal model delta sigma weight residual 1.236 1.185 0.050 1.21e-02 6.83e+03 1.74e+01 bond pdb=" CA LEU B 374 " pdb=" C LEU B 374 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.23e-02 6.61e+03 1.70e+01 bond pdb=" N LEU B 374 " pdb=" CA LEU B 374 " ideal model delta sigma weight residual 1.456 1.410 0.046 1.23e-02 6.61e+03 1.40e+01 bond pdb=" N PRO B 373 " pdb=" CA PRO B 373 " ideal model delta sigma weight residual 1.469 1.425 0.043 1.28e-02 6.10e+03 1.15e+01 bond pdb=" CA GLU A 420 " pdb=" CB GLU A 420 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.59e-02 3.96e+03 1.10e+01 ... (remaining 16888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 22554 2.26 - 4.52: 173 4.52 - 6.78: 20 6.78 - 9.04: 4 9.04 - 11.30: 1 Bond angle restraints: 22752 Sorted by residual: angle pdb=" C GLU B 372 " pdb=" N PRO B 373 " pdb=" CA PRO B 373 " ideal model delta sigma weight residual 119.84 115.24 4.60 1.25e+00 6.40e-01 1.36e+01 angle pdb=" N ILE C 476 " pdb=" CA ILE C 476 " pdb=" C ILE C 476 " ideal model delta sigma weight residual 111.91 108.63 3.28 8.90e-01 1.26e+00 1.35e+01 angle pdb=" N PHE B 377 " pdb=" CA PHE B 377 " pdb=" C PHE B 377 " ideal model delta sigma weight residual 111.82 107.81 4.01 1.16e+00 7.43e-01 1.19e+01 angle pdb=" C ASN C 271 " pdb=" N ILE C 272 " pdb=" CA ILE C 272 " ideal model delta sigma weight residual 122.97 119.59 3.38 9.80e-01 1.04e+00 1.19e+01 angle pdb=" C GLY A 371 " pdb=" N GLU A 372 " pdb=" CA GLU A 372 " ideal model delta sigma weight residual 122.15 110.85 11.30 3.47e+00 8.31e-02 1.06e+01 ... (remaining 22747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 8796 17.88 - 35.76: 1178 35.76 - 53.64: 287 53.64 - 71.52: 61 71.52 - 89.40: 25 Dihedral angle restraints: 10347 sinusoidal: 4345 harmonic: 6002 Sorted by residual: dihedral pdb=" CB CYS C 82 " pdb=" SG CYS C 82 " pdb=" SG CYS C 273 " pdb=" CB CYS C 273 " ideal model delta sinusoidal sigma weight residual 93.00 171.86 -78.86 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS B 82 " pdb=" SG CYS B 82 " pdb=" SG CYS B 273 " pdb=" CB CYS B 273 " ideal model delta sinusoidal sigma weight residual 93.00 167.83 -74.83 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CB CYS A 82 " pdb=" SG CYS A 82 " pdb=" SG CYS A 273 " pdb=" CB CYS A 273 " ideal model delta sinusoidal sigma weight residual 93.00 163.53 -70.53 1 1.00e+01 1.00e-02 6.40e+01 ... (remaining 10344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2159 0.059 - 0.118: 333 0.118 - 0.177: 20 0.177 - 0.236: 1 0.236 - 0.295: 1 Chirality restraints: 2514 Sorted by residual: chirality pdb=" CA GLU A 420 " pdb=" N GLU A 420 " pdb=" C GLU A 420 " pdb=" CB GLU A 420 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA PRO B 373 " pdb=" N PRO B 373 " pdb=" C PRO B 373 " pdb=" CB PRO B 373 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE B 101 " pdb=" N ILE B 101 " pdb=" C ILE B 101 " pdb=" CB ILE B 101 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 2511 not shown) Planarity restraints: 2888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 372 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 373 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 381 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.42e+00 pdb=" N PRO B 382 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 382 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 382 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 541 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" C ASN A 541 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN A 541 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 542 " 0.010 2.00e-02 2.50e+03 ... (remaining 2885 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2440 2.75 - 3.29: 15740 3.29 - 3.83: 27002 3.83 - 4.36: 32403 4.36 - 4.90: 55781 Nonbonded interactions: 133366 Sorted by model distance: nonbonded pdb=" OH TYR B 204 " pdb=" OD1 ASN B 386 " model vdw 2.218 3.040 nonbonded pdb=" OG SER C 247 " pdb=" OE1 GLU C 248 " model vdw 2.229 3.040 nonbonded pdb=" O LEU A 409 " pdb=" OG1 THR A 412 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR C 224 " pdb=" NH1 ARG C 262 " model vdw 2.237 3.120 nonbonded pdb=" O LEU A 374 " pdb=" NH2 ARG A 446 " model vdw 2.262 3.120 ... (remaining 133361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 34 through 388 or resid 391 through 478)) selection = (chain 'D' and (resid 34 through 274 or resid 294 through 478)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.040 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: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.690 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 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 : 0.004 0.053 16897 Z= 0.176 Angle : 0.540 11.295 22760 Z= 0.297 Chirality : 0.041 0.295 2514 Planarity : 0.004 0.049 2888 Dihedral : 17.175 89.396 6441 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.05 % Allowed : 19.07 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.19), residues: 2001 helix: 2.08 (0.15), residues: 1174 sheet: -0.06 (0.42), residues: 134 loop : -0.77 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 395 TYR 0.023 0.002 TYR B 228 PHE 0.018 0.002 PHE A 305 TRP 0.012 0.001 TRP A 480 HIS 0.005 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00375 (16893) covalent geometry : angle 0.53397 (22752) SS BOND : bond 0.00527 ( 4) SS BOND : angle 4.30599 ( 8) hydrogen bonds : bond 0.16989 ( 899) hydrogen bonds : angle 5.25009 ( 2661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LEU cc_start: 0.7967 (tp) cc_final: 0.7665 (tp) REVERT: A 547 LYS cc_start: 0.6157 (mmtt) cc_final: 0.4339 (tttm) REVERT: A 642 ARG cc_start: 0.6671 (tmm160) cc_final: 0.6345 (tmm-80) REVERT: B 486 LEU cc_start: 0.6947 (tp) cc_final: 0.6719 (tt) REVERT: C 465 PHE cc_start: 0.7249 (t80) cc_final: 0.6764 (t80) outliers start: 1 outliers final: 2 residues processed: 156 average time/residue: 0.7086 time to fit residues: 121.1769 Evaluate side-chains 141 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain B residue 505 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN D 271 ASN D 399 HIS ** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.152665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101090 restraints weight = 24433.012| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.00 r_work: 0.3106 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16897 Z= 0.120 Angle : 0.485 8.671 22760 Z= 0.266 Chirality : 0.039 0.138 2514 Planarity : 0.004 0.045 2888 Dihedral : 3.918 51.085 2221 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.42 % Allowed : 18.96 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.19), residues: 2001 helix: 2.35 (0.15), residues: 1193 sheet: 0.14 (0.43), residues: 130 loop : -0.63 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 571 TYR 0.024 0.001 TYR A 524 PHE 0.014 0.001 PHE A 305 TRP 0.010 0.001 TRP A 480 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00251 (16893) covalent geometry : angle 0.48367 (22752) SS BOND : bond 0.00346 ( 4) SS BOND : angle 1.92264 ( 8) hydrogen bonds : bond 0.05515 ( 899) hydrogen bonds : angle 4.15230 ( 2661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 ILE cc_start: 0.8500 (mt) cc_final: 0.8221 (mp) REVERT: A 547 LYS cc_start: 0.5649 (mmtt) cc_final: 0.3930 (tttt) REVERT: B 236 ILE cc_start: 0.7857 (mt) cc_final: 0.7651 (mp) REVERT: C 465 PHE cc_start: 0.8046 (t80) cc_final: 0.7269 (t80) outliers start: 26 outliers final: 7 residues processed: 183 average time/residue: 0.6283 time to fit residues: 127.4395 Evaluate side-chains 140 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain D residue 350 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 185 optimal weight: 0.0000 chunk 159 optimal weight: 0.0010 chunk 70 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN A 416 ASN D 399 HIS ** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.152733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101059 restraints weight = 24515.600| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.99 r_work: 0.3103 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16897 Z= 0.117 Angle : 0.477 8.385 22760 Z= 0.260 Chirality : 0.039 0.164 2514 Planarity : 0.004 0.069 2888 Dihedral : 3.893 51.742 2221 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.92 % Allowed : 19.12 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.19), residues: 2001 helix: 2.40 (0.15), residues: 1195 sheet: 0.28 (0.44), residues: 130 loop : -0.67 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 571 TYR 0.030 0.001 TYR A 524 PHE 0.015 0.001 PHE A 305 TRP 0.009 0.001 TRP D 208 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00257 (16893) covalent geometry : angle 0.47547 (22752) SS BOND : bond 0.00338 ( 4) SS BOND : angle 2.04790 ( 8) hydrogen bonds : bond 0.05046 ( 899) hydrogen bonds : angle 3.98388 ( 2661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 ILE cc_start: 0.8456 (mt) cc_final: 0.8209 (mp) REVERT: A 547 LYS cc_start: 0.5779 (mmtt) cc_final: 0.4174 (tttt) REVERT: C 34 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.5462 (pp-130) REVERT: C 274 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8068 (ttpt) REVERT: C 465 PHE cc_start: 0.8068 (t80) cc_final: 0.7268 (t80) REVERT: D 65 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8394 (ptp90) REVERT: D 235 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6588 (mm-30) outliers start: 35 outliers final: 9 residues processed: 179 average time/residue: 0.6492 time to fit residues: 128.3939 Evaluate side-chains 150 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 350 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 170 optimal weight: 0.5980 chunk 186 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN A 416 ASN B 513 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.150844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.098859 restraints weight = 24406.671| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.97 r_work: 0.3056 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16897 Z= 0.165 Angle : 0.523 9.212 22760 Z= 0.284 Chirality : 0.041 0.164 2514 Planarity : 0.004 0.044 2888 Dihedral : 4.068 50.254 2221 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.14 % Allowed : 20.38 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.19), residues: 2001 helix: 2.25 (0.15), residues: 1199 sheet: 0.26 (0.44), residues: 132 loop : -0.71 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 571 TYR 0.035 0.002 TYR A 524 PHE 0.018 0.002 PHE B 465 TRP 0.010 0.001 TRP A 480 HIS 0.006 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00392 (16893) covalent geometry : angle 0.52010 (22752) SS BOND : bond 0.00364 ( 4) SS BOND : angle 2.99421 ( 8) hydrogen bonds : bond 0.05901 ( 899) hydrogen bonds : angle 4.05513 ( 2661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 LYS cc_start: 0.5814 (mmtt) cc_final: 0.4152 (tmtt) REVERT: B 437 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8278 (mtpp) REVERT: B 513 HIS cc_start: 0.8304 (t70) cc_final: 0.8069 (t-170) REVERT: C 34 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.5572 (pp-130) REVERT: C 274 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8063 (ttpt) REVERT: C 465 PHE cc_start: 0.8087 (t80) cc_final: 0.7300 (t80) REVERT: D 65 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8417 (ptp90) REVERT: D 235 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6604 (mm-30) outliers start: 39 outliers final: 17 residues processed: 176 average time/residue: 0.6996 time to fit residues: 135.8033 Evaluate side-chains 159 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 350 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 189 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 152 optimal weight: 0.0870 chunk 118 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN A 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101246 restraints weight = 24337.473| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.99 r_work: 0.3107 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16897 Z= 0.109 Angle : 0.477 8.339 22760 Z= 0.256 Chirality : 0.038 0.160 2514 Planarity : 0.004 0.087 2888 Dihedral : 3.882 51.214 2221 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.08 % Allowed : 20.99 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.19), residues: 2001 helix: 2.41 (0.15), residues: 1201 sheet: 0.31 (0.44), residues: 130 loop : -0.71 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 571 TYR 0.032 0.001 TYR A 524 PHE 0.015 0.001 PHE A 552 TRP 0.008 0.001 TRP D 208 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00238 (16893) covalent geometry : angle 0.47485 (22752) SS BOND : bond 0.00281 ( 4) SS BOND : angle 2.58314 ( 8) hydrogen bonds : bond 0.04664 ( 899) hydrogen bonds : angle 3.92155 ( 2661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 528 ARG cc_start: 0.7414 (mmm-85) cc_final: 0.7134 (tpt-90) REVERT: A 547 LYS cc_start: 0.5720 (mmtt) cc_final: 0.4196 (tttt) REVERT: B 513 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.8080 (t-170) REVERT: C 34 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.5739 (pp-130) REVERT: C 308 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8875 (tt) REVERT: C 465 PHE cc_start: 0.8070 (t80) cc_final: 0.7291 (t80) REVERT: D 65 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8399 (ptp90) REVERT: D 235 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6552 (mm-30) outliers start: 38 outliers final: 15 residues processed: 178 average time/residue: 0.6557 time to fit residues: 129.6723 Evaluate side-chains 153 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 513 HIS Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 350 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 11 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 chunk 196 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN B 513 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.152090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100307 restraints weight = 24336.464| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.98 r_work: 0.3085 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16897 Z= 0.129 Angle : 0.490 9.370 22760 Z= 0.264 Chirality : 0.039 0.159 2514 Planarity : 0.004 0.046 2888 Dihedral : 3.906 51.155 2221 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.19 % Allowed : 21.59 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.19), residues: 2001 helix: 2.38 (0.15), residues: 1201 sheet: 0.30 (0.44), residues: 130 loop : -0.73 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 571 TYR 0.037 0.002 TYR A 524 PHE 0.015 0.002 PHE A 305 TRP 0.009 0.001 TRP D 208 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00299 (16893) covalent geometry : angle 0.48863 (22752) SS BOND : bond 0.00317 ( 4) SS BOND : angle 1.80791 ( 8) hydrogen bonds : bond 0.05068 ( 899) hydrogen bonds : angle 3.93865 ( 2661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 528 ARG cc_start: 0.7379 (mmm-85) cc_final: 0.7093 (tpt-90) REVERT: A 547 LYS cc_start: 0.5749 (mmtt) cc_final: 0.4161 (tmtt) REVERT: C 34 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.5530 (pp-130) REVERT: C 308 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8900 (tt) REVERT: C 465 PHE cc_start: 0.8099 (t80) cc_final: 0.7327 (t80) REVERT: D 65 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8424 (ptp90) REVERT: D 147 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: D 235 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6535 (mm-30) outliers start: 40 outliers final: 23 residues processed: 172 average time/residue: 0.6581 time to fit residues: 125.7160 Evaluate side-chains 160 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 350 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 0.0370 chunk 148 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 131 optimal weight: 0.0270 chunk 56 optimal weight: 10.0000 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN B 223 HIS B 513 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.153129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101489 restraints weight = 24349.132| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.99 r_work: 0.3105 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16897 Z= 0.113 Angle : 0.488 9.511 22760 Z= 0.260 Chirality : 0.038 0.158 2514 Planarity : 0.004 0.091 2888 Dihedral : 3.837 51.411 2221 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.14 % Allowed : 22.03 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.19), residues: 2001 helix: 2.44 (0.15), residues: 1203 sheet: 0.31 (0.44), residues: 130 loop : -0.72 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 571 TYR 0.034 0.001 TYR A 524 PHE 0.015 0.001 PHE B 534 TRP 0.008 0.001 TRP D 208 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00255 (16893) covalent geometry : angle 0.48399 (22752) SS BOND : bond 0.00357 ( 4) SS BOND : angle 3.22304 ( 8) hydrogen bonds : bond 0.04609 ( 899) hydrogen bonds : angle 3.87933 ( 2661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 547 LYS cc_start: 0.5838 (mmtt) cc_final: 0.4309 (tttt) REVERT: B 304 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8280 (mtpt) REVERT: C 34 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.5550 (pp-130) REVERT: C 308 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8907 (tt) REVERT: C 465 PHE cc_start: 0.8071 (t80) cc_final: 0.7329 (t80) REVERT: D 65 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8396 (ptp90) REVERT: D 235 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6548 (mm-30) outliers start: 39 outliers final: 21 residues processed: 174 average time/residue: 0.6662 time to fit residues: 128.8386 Evaluate side-chains 159 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 350 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 24 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 140 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 400 GLN B 513 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.150917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098923 restraints weight = 24353.095| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.97 r_work: 0.3049 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16897 Z= 0.169 Angle : 0.536 10.066 22760 Z= 0.288 Chirality : 0.041 0.163 2514 Planarity : 0.004 0.043 2888 Dihedral : 4.031 50.660 2221 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.25 % Allowed : 22.14 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.19), residues: 2001 helix: 2.27 (0.15), residues: 1202 sheet: 0.23 (0.43), residues: 132 loop : -0.75 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 571 TYR 0.037 0.002 TYR A 524 PHE 0.017 0.002 PHE B 465 TRP 0.009 0.001 TRP A 480 HIS 0.005 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00408 (16893) covalent geometry : angle 0.53172 (22752) SS BOND : bond 0.00337 ( 4) SS BOND : angle 3.81914 ( 8) hydrogen bonds : bond 0.05790 ( 899) hydrogen bonds : angle 4.01690 ( 2661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 LYS cc_start: 0.5771 (mmtt) cc_final: 0.4172 (tmtt) REVERT: A 571 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7683 (mtt90) REVERT: B 304 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8260 (mtpt) REVERT: C 34 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.5555 (pp-130) REVERT: C 308 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8945 (tt) REVERT: C 465 PHE cc_start: 0.8089 (t80) cc_final: 0.7322 (t80) REVERT: D 49 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8235 (mm-30) REVERT: D 65 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8437 (ptp90) REVERT: D 147 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: D 235 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6581 (mm-30) REVERT: D 336 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9148 (tp) outliers start: 41 outliers final: 23 residues processed: 171 average time/residue: 0.6742 time to fit residues: 127.7354 Evaluate side-chains 161 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 350 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 18 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 43 optimal weight: 0.0470 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 0.2980 chunk 158 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS C 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.154232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102831 restraints weight = 24396.869| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.00 r_work: 0.3133 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16897 Z= 0.101 Angle : 0.481 10.595 22760 Z= 0.256 Chirality : 0.038 0.156 2514 Planarity : 0.004 0.043 2888 Dihedral : 3.769 51.223 2221 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.53 % Allowed : 22.96 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.19), residues: 2001 helix: 2.49 (0.15), residues: 1204 sheet: 0.32 (0.44), residues: 130 loop : -0.73 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 571 TYR 0.033 0.001 TYR A 524 PHE 0.013 0.001 PHE A 305 TRP 0.009 0.001 TRP C 208 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00217 (16893) covalent geometry : angle 0.47808 (22752) SS BOND : bond 0.00385 ( 4) SS BOND : angle 2.92062 ( 8) hydrogen bonds : bond 0.04153 ( 899) hydrogen bonds : angle 3.84270 ( 2661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 547 LYS cc_start: 0.5790 (mmtt) cc_final: 0.4276 (tttt) REVERT: A 571 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7627 (mtt90) REVERT: B 304 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8265 (mtpt) REVERT: C 274 LYS cc_start: 0.8375 (ttpt) cc_final: 0.8004 (mppt) REVERT: C 308 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8912 (tt) REVERT: C 465 PHE cc_start: 0.8058 (t80) cc_final: 0.7335 (t80) REVERT: D 34 MET cc_start: 0.8037 (ttp) cc_final: 0.7682 (ttt) REVERT: D 49 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8120 (mm-30) REVERT: D 65 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8357 (ptp90) outliers start: 28 outliers final: 13 residues processed: 169 average time/residue: 0.6832 time to fit residues: 127.4703 Evaluate side-chains 149 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 271 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 73 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 0.0010 chunk 94 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 513 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101518 restraints weight = 24369.337| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.99 r_work: 0.3103 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16897 Z= 0.113 Angle : 0.491 10.443 22760 Z= 0.265 Chirality : 0.039 0.152 2514 Planarity : 0.004 0.042 2888 Dihedral : 3.776 51.756 2221 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.10 % Allowed : 23.56 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.19), residues: 2001 helix: 2.49 (0.15), residues: 1203 sheet: 0.38 (0.44), residues: 130 loop : -0.72 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 571 TYR 0.037 0.001 TYR A 524 PHE 0.014 0.001 PHE A 305 TRP 0.008 0.001 TRP D 208 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00256 (16893) covalent geometry : angle 0.48883 (22752) SS BOND : bond 0.00319 ( 4) SS BOND : angle 2.59348 ( 8) hydrogen bonds : bond 0.04538 ( 899) hydrogen bonds : angle 3.85063 ( 2661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 547 LYS cc_start: 0.5784 (mmtt) cc_final: 0.4262 (tttt) REVERT: A 571 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7557 (mtt90) REVERT: B 304 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8276 (mtpt) REVERT: B 534 PHE cc_start: 0.7578 (m-10) cc_final: 0.7377 (m-10) REVERT: C 274 LYS cc_start: 0.8403 (ttpt) cc_final: 0.8040 (mppt) REVERT: C 308 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8912 (tt) REVERT: C 465 PHE cc_start: 0.8067 (t80) cc_final: 0.7358 (t80) REVERT: D 49 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8186 (mm-30) REVERT: D 65 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8378 (ptp90) outliers start: 20 outliers final: 15 residues processed: 152 average time/residue: 0.6789 time to fit residues: 114.3468 Evaluate side-chains 151 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 447 ARG Chi-restraints excluded: chain D residue 65 ARG Chi-restraints excluded: chain D residue 271 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 167 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 111 optimal weight: 0.0370 chunk 95 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS D 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.152313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099861 restraints weight = 24107.314| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.01 r_work: 0.3082 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16897 Z= 0.135 Angle : 0.512 10.798 22760 Z= 0.275 Chirality : 0.039 0.156 2514 Planarity : 0.004 0.042 2888 Dihedral : 3.876 50.756 2221 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.32 % Allowed : 23.45 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.19), residues: 2001 helix: 2.41 (0.15), residues: 1204 sheet: 0.35 (0.44), residues: 130 loop : -0.73 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 571 TYR 0.035 0.002 TYR A 524 PHE 0.015 0.002 PHE A 305 TRP 0.008 0.001 TRP D 208 HIS 0.004 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00319 (16893) covalent geometry : angle 0.50956 (22752) SS BOND : bond 0.00417 ( 4) SS BOND : angle 2.64292 ( 8) hydrogen bonds : bond 0.05074 ( 899) hydrogen bonds : angle 3.92015 ( 2661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6595.13 seconds wall clock time: 113 minutes 4.52 seconds (6784.52 seconds total)