Starting phenix.real_space_refine on Wed Sep 17 15:20:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvw_61845/09_2025/9jvw_61845.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvw_61845/09_2025/9jvw_61845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jvw_61845/09_2025/9jvw_61845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvw_61845/09_2025/9jvw_61845.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvw_61845/09_2025/9jvw_61845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvw_61845/09_2025/9jvw_61845.cif" } resolution = 3.41 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= 0.022 sd= 0.159 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: 6 Type Number sf(0) Gaussians Br 3 7.06 5 S 72 5.16 5 C 6249 2.51 5 N 1503 2.21 5 O 1647 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9480 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3107 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 13, 'TRANS': 401} Chain breaks: 2 Chain: "B" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3107 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 13, 'TRANS': 401} Chain breaks: 2 Chain: "C" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3107 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 13, 'TRANS': 401} Chain breaks: 2 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'CLR': 1, 'GJ0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'CLR': 1, 'GJ0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'CLR': 1, 'GJ0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.38, per 1000 atoms: 0.25 Number of scatterers: 9480 At special positions: 0 Unit cell: (113.085, 114.162, 81.852, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 3 34.99 S 72 16.00 F 6 9.00 O 1647 8.00 N 1503 7.00 C 6249 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 316.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 83.9% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 46 through 65 Processing helix chain 'A' and resid 71 through 91 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 92 through 106 removed outlier: 3.506A pdb=" N LEU A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 143 removed outlier: 4.159A pdb=" N THR A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.790A pdb=" N PHE A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 Processing helix chain 'A' and resid 241 through 258 removed outlier: 3.653A pdb=" N LEU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 302 removed outlier: 3.854A pdb=" N VAL A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.831A pdb=" N ALA A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 341 removed outlier: 3.864A pdb=" N GLN A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 4.029A pdb=" N VAL A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.994A pdb=" N PHE A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 379 removed outlier: 3.697A pdb=" N ARG A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 397 removed outlier: 3.534A pdb=" N ARG A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Proline residue: A 391 - end of helix removed outlier: 4.518A pdb=" N THR A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.517A pdb=" N ALA A 402 " --> pdb=" O MET A 398 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 442 removed outlier: 4.071A pdb=" N VAL A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 460 through 463 removed outlier: 4.049A pdb=" N ASP A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.649A pdb=" N ALA A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 473 Processing helix chain 'A' and resid 474 through 496 removed outlier: 4.235A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 481 " --> pdb=" O MET A 477 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 removed outlier: 3.701A pdb=" N LEU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 65 Processing helix chain 'B' and resid 71 through 91 Proline residue: B 81 - end of helix Processing helix chain 'B' and resid 92 through 106 removed outlier: 3.507A pdb=" N LEU B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 143 removed outlier: 4.160A pdb=" N THR B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 removed outlier: 3.789A pdb=" N PHE B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 Processing helix chain 'B' and resid 241 through 258 removed outlier: 3.652A pdb=" N LEU B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 302 removed outlier: 3.852A pdb=" N VAL B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Proline residue: B 289 - end of helix removed outlier: 3.830A pdb=" N ALA B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 341 removed outlier: 3.864A pdb=" N GLN B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 4.030A pdb=" N VAL B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.993A pdb=" N PHE B 347 " --> pdb=" O ASN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 379 removed outlier: 3.698A pdb=" N ARG B 373 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 397 removed outlier: 3.533A pdb=" N ARG B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Proline residue: B 391 - end of helix removed outlier: 4.519A pdb=" N THR B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.518A pdb=" N ALA B 402 " --> pdb=" O MET B 398 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 442 removed outlier: 4.072A pdb=" N VAL B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 437 " --> pdb=" O THR B 433 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 440 " --> pdb=" O SER B 436 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 457 Processing helix chain 'B' and resid 460 through 463 removed outlier: 4.049A pdb=" N ASP B 463 " --> pdb=" O PRO B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 463' Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.648A pdb=" N ALA B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 473 Processing helix chain 'B' and resid 474 through 496 removed outlier: 4.235A pdb=" N SER B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 481 " --> pdb=" O MET B 477 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS B 495 " --> pdb=" O GLY B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 506 removed outlier: 3.701A pdb=" N LEU B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 65 Processing helix chain 'C' and resid 71 through 91 Proline residue: C 81 - end of helix Processing helix chain 'C' and resid 92 through 106 removed outlier: 3.508A pdb=" N LEU C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 102 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 143 removed outlier: 4.160A pdb=" N THR C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 128 " --> pdb=" O TYR C 124 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 removed outlier: 3.790A pdb=" N PHE C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 Processing helix chain 'C' and resid 241 through 258 removed outlier: 3.653A pdb=" N LEU C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 302 removed outlier: 3.853A pdb=" N VAL C 267 " --> pdb=" O ALA C 263 " (cutoff:3.500A) Proline residue: C 289 - end of helix removed outlier: 3.831A pdb=" N ALA C 293 " --> pdb=" O PRO C 289 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 341 removed outlier: 3.864A pdb=" N GLN C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Proline residue: C 333 - end of helix removed outlier: 4.030A pdb=" N VAL C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.993A pdb=" N PHE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.698A pdb=" N ARG C 373 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU C 377 " --> pdb=" O ARG C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 397 removed outlier: 3.534A pdb=" N ARG C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE C 388 " --> pdb=" O ARG C 384 " (cutoff:3.500A) Proline residue: C 391 - end of helix removed outlier: 4.519A pdb=" N THR C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 416 removed outlier: 3.517A pdb=" N ALA C 402 " --> pdb=" O MET C 398 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 442 removed outlier: 4.071A pdb=" N VAL C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 437 " --> pdb=" O THR C 433 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA C 440 " --> pdb=" O SER C 436 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 441 " --> pdb=" O VAL C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 457 Processing helix chain 'C' and resid 460 through 463 removed outlier: 4.048A pdb=" N ASP C 463 " --> pdb=" O PRO C 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 460 through 463' Processing helix chain 'C' and resid 464 through 469 removed outlier: 3.648A pdb=" N ALA C 469 " --> pdb=" O SER C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 474 through 496 removed outlier: 4.235A pdb=" N SER C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 481 " --> pdb=" O MET C 477 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS C 495 " --> pdb=" O GLY C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 506 removed outlier: 3.700A pdb=" N LEU C 501 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 189 Processing sheet with id=AA2, first strand: chain 'B' and resid 186 through 189 Processing sheet with id=AA3, first strand: chain 'C' and resid 186 through 189 648 hydrogen bonds defined for protein. 1917 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: 1.51 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 2876 1.34 - 1.49: 2400 1.49 - 1.64: 4228 1.64 - 1.79: 72 1.79 - 1.94: 60 Bond restraints: 9636 Sorted by residual: bond pdb=" C13 GJ0 C1002 " pdb=" C14 GJ0 C1002 " ideal model delta sigma weight residual 1.511 1.425 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C13 GJ0 B1002 " pdb=" C14 GJ0 B1002 " ideal model delta sigma weight residual 1.511 1.425 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C13 GJ0 A1002 " pdb=" C14 GJ0 A1002 " ideal model delta sigma weight residual 1.511 1.426 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C23 GJ0 B1002 " pdb="BR GJ0 B1002 " ideal model delta sigma weight residual 1.878 1.942 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C23 GJ0 C1002 " pdb="BR GJ0 C1002 " ideal model delta sigma weight residual 1.878 1.942 -0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 9631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 12840 3.10 - 6.21: 193 6.21 - 9.31: 32 9.31 - 12.41: 24 12.41 - 15.52: 3 Bond angle restraints: 13092 Sorted by residual: angle pdb=" N SER B 288 " pdb=" CA SER B 288 " pdb=" C SER B 288 " ideal model delta sigma weight residual 109.81 121.29 -11.48 2.21e+00 2.05e-01 2.70e+01 angle pdb=" N SER C 288 " pdb=" CA SER C 288 " pdb=" C SER C 288 " ideal model delta sigma weight residual 109.81 121.29 -11.48 2.21e+00 2.05e-01 2.70e+01 angle pdb=" N SER A 288 " pdb=" CA SER A 288 " pdb=" C SER A 288 " ideal model delta sigma weight residual 109.81 121.29 -11.48 2.21e+00 2.05e-01 2.70e+01 angle pdb=" C11 GJ0 C1002 " pdb=" N12 GJ0 C1002 " pdb=" C13 GJ0 C1002 " ideal model delta sigma weight residual 129.20 113.68 15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C11 GJ0 B1002 " pdb=" N12 GJ0 B1002 " pdb=" C13 GJ0 B1002 " ideal model delta sigma weight residual 129.20 113.71 15.49 3.00e+00 1.11e-01 2.66e+01 ... (remaining 13087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5238 17.86 - 35.73: 501 35.73 - 53.59: 81 53.59 - 71.46: 18 71.46 - 89.32: 12 Dihedral angle restraints: 5850 sinusoidal: 2343 harmonic: 3507 Sorted by residual: dihedral pdb=" CA SER C 68 " pdb=" C SER C 68 " pdb=" N PRO C 69 " pdb=" CA PRO C 69 " ideal model delta harmonic sigma weight residual 180.00 162.44 17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA SER A 68 " pdb=" C SER A 68 " pdb=" N PRO A 69 " pdb=" CA PRO A 69 " ideal model delta harmonic sigma weight residual 180.00 162.46 17.54 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA SER B 68 " pdb=" C SER B 68 " pdb=" N PRO B 69 " pdb=" CA PRO B 69 " ideal model delta harmonic sigma weight residual 180.00 162.52 17.48 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.281: 1656 0.281 - 0.563: 0 0.563 - 0.844: 0 0.844 - 1.126: 0 1.126 - 1.407: 3 Chirality restraints: 1659 Sorted by residual: chirality pdb=" C15 GJ0 A1002 " pdb=" C14 GJ0 A1002 " pdb=" C17 GJ0 A1002 " pdb=" N16 GJ0 A1002 " both_signs ideal model delta sigma weight residual False -2.46 -1.05 -1.41 2.00e-01 2.50e+01 4.95e+01 chirality pdb=" C15 GJ0 B1002 " pdb=" C14 GJ0 B1002 " pdb=" C17 GJ0 B1002 " pdb=" N16 GJ0 B1002 " both_signs ideal model delta sigma weight residual False -2.46 -1.05 -1.41 2.00e-01 2.50e+01 4.94e+01 chirality pdb=" C15 GJ0 C1002 " pdb=" C14 GJ0 C1002 " pdb=" C17 GJ0 C1002 " pdb=" N16 GJ0 C1002 " both_signs ideal model delta sigma weight residual False -2.46 -1.05 -1.41 2.00e-01 2.50e+01 4.94e+01 ... (remaining 1656 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 GJ0 C1002 " 0.020 2.00e-02 2.50e+03 3.88e-02 3.00e+01 pdb=" C11 GJ0 C1002 " -0.074 2.00e-02 2.50e+03 pdb=" C21 GJ0 C1002 " 0.010 2.00e-02 2.50e+03 pdb=" C22 GJ0 C1002 " 0.001 2.00e-02 2.50e+03 pdb=" C8 GJ0 C1002 " -0.048 2.00e-02 2.50e+03 pdb=" C9 GJ0 C1002 " 0.007 2.00e-02 2.50e+03 pdb=" N12 GJ0 C1002 " 0.047 2.00e-02 2.50e+03 pdb=" O7 GJ0 C1002 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 GJ0 B1002 " -0.020 2.00e-02 2.50e+03 3.87e-02 3.00e+01 pdb=" C11 GJ0 B1002 " 0.074 2.00e-02 2.50e+03 pdb=" C21 GJ0 B1002 " -0.010 2.00e-02 2.50e+03 pdb=" C22 GJ0 B1002 " -0.001 2.00e-02 2.50e+03 pdb=" C8 GJ0 B1002 " 0.049 2.00e-02 2.50e+03 pdb=" C9 GJ0 B1002 " -0.007 2.00e-02 2.50e+03 pdb=" N12 GJ0 B1002 " -0.047 2.00e-02 2.50e+03 pdb=" O7 GJ0 B1002 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 GJ0 A1002 " -0.019 2.00e-02 2.50e+03 3.87e-02 3.00e+01 pdb=" C11 GJ0 A1002 " 0.074 2.00e-02 2.50e+03 pdb=" C21 GJ0 A1002 " -0.010 2.00e-02 2.50e+03 pdb=" C22 GJ0 A1002 " -0.000 2.00e-02 2.50e+03 pdb=" C8 GJ0 A1002 " 0.048 2.00e-02 2.50e+03 pdb=" C9 GJ0 A1002 " -0.007 2.00e-02 2.50e+03 pdb=" N12 GJ0 A1002 " -0.047 2.00e-02 2.50e+03 pdb=" O7 GJ0 A1002 " -0.039 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1331 2.75 - 3.29: 9072 3.29 - 3.82: 15139 3.82 - 4.36: 18111 4.36 - 4.90: 31582 Nonbonded interactions: 75235 Sorted by model distance: nonbonded pdb=" OD2 ASP A 471 " pdb=" C23 GJ0 A1002 " model vdw 2.210 3.270 nonbonded pdb=" OD2 ASP B 471 " pdb=" C23 GJ0 B1002 " model vdw 2.210 3.270 nonbonded pdb=" OD2 ASP C 471 " pdb=" C23 GJ0 C1002 " model vdw 2.210 3.270 nonbonded pdb=" ND2 ASN B 482 " pdb=" O18 GJ0 B1002 " model vdw 2.257 3.120 nonbonded pdb=" ND2 ASN A 482 " pdb=" O18 GJ0 A1002 " model vdw 2.258 3.120 ... (remaining 75230 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.310 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 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 : 0.008 0.086 9636 Z= 0.343 Angle : 1.116 15.516 13092 Z= 0.574 Chirality : 0.082 1.407 1659 Planarity : 0.007 0.050 1572 Dihedral : 14.785 89.321 3600 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.29 % Allowed : 6.00 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.94 (0.18), residues: 1227 helix: -2.44 (0.12), residues: 900 sheet: -2.91 (0.89), residues: 36 loop : -2.33 (0.29), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 311 TYR 0.013 0.003 TYR B 316 PHE 0.020 0.002 PHE B 348 TRP 0.020 0.002 TRP A 472 HIS 0.006 0.002 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00804 ( 9636) covalent geometry : angle 1.11646 (13092) hydrogen bonds : bond 0.17956 ( 648) hydrogen bonds : angle 7.19689 ( 1917) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 265 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7071 (t0) cc_final: 0.6855 (t0) REVERT: A 98 ILE cc_start: 0.7603 (mt) cc_final: 0.7095 (pt) REVERT: A 125 MET cc_start: 0.7225 (mmt) cc_final: 0.5928 (ptp) REVERT: B 71 HIS cc_start: 0.7677 (t-90) cc_final: 0.7448 (t-170) REVERT: B 73 ASP cc_start: 0.7691 (m-30) cc_final: 0.7470 (m-30) REVERT: B 98 ILE cc_start: 0.7476 (mt) cc_final: 0.7263 (mt) REVERT: B 121 MET cc_start: 0.8281 (mmt) cc_final: 0.8080 (mmt) REVERT: B 125 MET cc_start: 0.6732 (mmt) cc_final: 0.5876 (ptm) REVERT: B 189 GLN cc_start: 0.6997 (pt0) cc_final: 0.6762 (pt0) REVERT: B 311 ARG cc_start: 0.6718 (ttm170) cc_final: 0.5963 (ttt90) REVERT: C 73 ASP cc_start: 0.7781 (m-30) cc_final: 0.7540 (m-30) REVERT: C 98 ILE cc_start: 0.7832 (mt) cc_final: 0.7352 (mt) REVERT: C 102 ILE cc_start: 0.8235 (mt) cc_final: 0.7988 (tp) REVERT: C 121 MET cc_start: 0.8491 (mmt) cc_final: 0.8047 (mmt) REVERT: C 125 MET cc_start: 0.7457 (mmt) cc_final: 0.6214 (ptm) outliers start: 3 outliers final: 3 residues processed: 268 average time/residue: 0.0956 time to fit residues: 36.2653 Evaluate side-chains 199 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 196 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 419 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 271 ASN A 327 HIS B 327 HIS ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 327 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.194205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.147867 restraints weight = 9742.961| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.95 r_work: 0.3250 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9636 Z= 0.130 Angle : 0.633 9.886 13092 Z= 0.314 Chirality : 0.040 0.141 1659 Planarity : 0.004 0.040 1572 Dihedral : 10.058 81.070 1527 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.46 % Allowed : 14.26 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.23), residues: 1227 helix: -0.47 (0.17), residues: 936 sheet: -3.00 (0.86), residues: 36 loop : -2.32 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 87 TYR 0.009 0.001 TYR A 316 PHE 0.021 0.001 PHE B 388 TRP 0.012 0.001 TRP B 472 HIS 0.009 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9636) covalent geometry : angle 0.63315 (13092) hydrogen bonds : bond 0.03936 ( 648) hydrogen bonds : angle 4.87083 ( 1917) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8047 (t0) cc_final: 0.7764 (t0) REVERT: A 125 MET cc_start: 0.6876 (mmt) cc_final: 0.5790 (ptm) REVERT: A 173 ARG cc_start: 0.7086 (mtt180) cc_final: 0.6694 (mtt-85) REVERT: A 325 ILE cc_start: 0.8670 (mm) cc_final: 0.8465 (mm) REVERT: A 478 ARG cc_start: 0.8409 (mtm180) cc_final: 0.8205 (mtm180) REVERT: B 98 ILE cc_start: 0.8165 (mt) cc_final: 0.7824 (pt) REVERT: B 125 MET cc_start: 0.6360 (mmt) cc_final: 0.5655 (ptm) REVERT: B 259 MET cc_start: 0.6277 (mtt) cc_final: 0.6043 (mtm) REVERT: B 336 TYR cc_start: 0.7806 (t80) cc_final: 0.7562 (t80) REVERT: B 498 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6764 (mtmm) REVERT: C 98 ILE cc_start: 0.8309 (mt) cc_final: 0.7943 (pt) REVERT: C 121 MET cc_start: 0.8040 (mmt) cc_final: 0.7794 (mmt) REVERT: C 125 MET cc_start: 0.7271 (mmt) cc_final: 0.5751 (ttp) REVERT: C 234 LEU cc_start: 0.7361 (mt) cc_final: 0.7141 (mp) REVERT: C 498 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7157 (mtmm) outliers start: 25 outliers final: 19 residues processed: 216 average time/residue: 0.0839 time to fit residues: 26.4853 Evaluate side-chains 195 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 498 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN C 71 HIS C 174 ASN C 271 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.190558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140464 restraints weight = 9708.608| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.15 r_work: 0.3187 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9636 Z= 0.131 Angle : 0.598 8.419 13092 Z= 0.298 Chirality : 0.041 0.169 1659 Planarity : 0.004 0.039 1572 Dihedral : 8.329 77.558 1527 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.95 % Allowed : 18.58 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.24), residues: 1227 helix: 0.12 (0.18), residues: 960 sheet: -3.02 (0.81), residues: 36 loop : -2.07 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 87 TYR 0.014 0.001 TYR C 336 PHE 0.013 0.001 PHE B 252 TRP 0.011 0.001 TRP C 472 HIS 0.008 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9636) covalent geometry : angle 0.59788 (13092) hydrogen bonds : bond 0.03649 ( 648) hydrogen bonds : angle 4.60307 ( 1917) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8093 (t0) cc_final: 0.7783 (t0) REVERT: A 125 MET cc_start: 0.7009 (mmt) cc_final: 0.5895 (ptt) REVERT: A 325 ILE cc_start: 0.8665 (mm) cc_final: 0.8418 (mm) REVERT: A 387 ARG cc_start: 0.7304 (mmt180) cc_final: 0.6926 (mpt180) REVERT: B 98 ILE cc_start: 0.8380 (mt) cc_final: 0.7969 (pt) REVERT: B 125 MET cc_start: 0.6414 (mmt) cc_final: 0.5630 (ptm) REVERT: B 259 MET cc_start: 0.6499 (mtt) cc_final: 0.6275 (mtm) REVERT: B 315 MET cc_start: 0.6583 (mmt) cc_final: 0.6353 (tpp) REVERT: B 498 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6859 (mtmm) REVERT: C 98 ILE cc_start: 0.8436 (mt) cc_final: 0.7845 (pt) REVERT: C 121 MET cc_start: 0.8096 (mmt) cc_final: 0.7881 (mmm) REVERT: C 125 MET cc_start: 0.7030 (mmt) cc_final: 0.5873 (ptm) REVERT: C 498 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7361 (mtmm) outliers start: 30 outliers final: 22 residues processed: 198 average time/residue: 0.0878 time to fit residues: 25.1003 Evaluate side-chains 193 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 498 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.189366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139764 restraints weight = 9761.499| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.09 r_work: 0.3188 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9636 Z= 0.151 Angle : 0.624 8.520 13092 Z= 0.306 Chirality : 0.041 0.151 1659 Planarity : 0.004 0.032 1572 Dihedral : 7.733 73.444 1527 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.54 % Allowed : 21.14 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.25), residues: 1227 helix: 0.59 (0.18), residues: 921 sheet: -2.09 (0.85), residues: 30 loop : -1.68 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.012 0.001 TYR C 494 PHE 0.012 0.001 PHE A 249 TRP 0.010 0.001 TRP A 472 HIS 0.005 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9636) covalent geometry : angle 0.62370 (13092) hydrogen bonds : bond 0.03666 ( 648) hydrogen bonds : angle 4.59611 ( 1917) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.7178 (mmt) cc_final: 0.5914 (ptt) REVERT: A 325 ILE cc_start: 0.8708 (mm) cc_final: 0.8459 (mm) REVERT: A 498 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6963 (mtmm) REVERT: B 77 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7455 (tt) REVERT: B 125 MET cc_start: 0.6627 (mmt) cc_final: 0.5730 (ptm) REVERT: B 234 LEU cc_start: 0.7857 (mt) cc_final: 0.7646 (mt) REVERT: B 311 ARG cc_start: 0.6753 (ttm170) cc_final: 0.5947 (ttt90) REVERT: B 315 MET cc_start: 0.6499 (mmt) cc_final: 0.6283 (tpp) REVERT: B 498 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6807 (mtmm) REVERT: C 121 MET cc_start: 0.8019 (mmt) cc_final: 0.7778 (mmm) REVERT: C 125 MET cc_start: 0.7068 (mmt) cc_final: 0.5964 (ptm) REVERT: C 265 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7121 (tt) outliers start: 36 outliers final: 29 residues processed: 205 average time/residue: 0.0856 time to fit residues: 25.3857 Evaluate side-chains 211 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 428 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 99 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 98 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.192051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.141730 restraints weight = 9632.785| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.99 r_work: 0.3243 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9636 Z= 0.108 Angle : 0.563 9.294 13092 Z= 0.278 Chirality : 0.039 0.157 1659 Planarity : 0.003 0.031 1572 Dihedral : 7.391 72.793 1527 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.85 % Allowed : 21.73 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.25), residues: 1227 helix: 0.94 (0.18), residues: 927 sheet: -1.97 (0.85), residues: 30 loop : -1.46 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 87 TYR 0.014 0.001 TYR B 494 PHE 0.010 0.001 PHE C 252 TRP 0.008 0.001 TRP A 472 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9636) covalent geometry : angle 0.56348 (13092) hydrogen bonds : bond 0.03148 ( 648) hydrogen bonds : angle 4.36281 ( 1917) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.8789 (mm) cc_final: 0.8581 (mm) REVERT: A 125 MET cc_start: 0.6755 (mmt) cc_final: 0.5809 (ptm) REVERT: A 325 ILE cc_start: 0.8714 (mm) cc_final: 0.8462 (mm) REVERT: A 467 LEU cc_start: 0.6401 (mp) cc_final: 0.6185 (mt) REVERT: A 477 MET cc_start: 0.6971 (mmt) cc_final: 0.6708 (mmt) REVERT: B 48 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7615 (t) REVERT: B 125 MET cc_start: 0.6322 (mmt) cc_final: 0.5846 (ptm) REVERT: B 498 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6844 (mtmm) REVERT: C 98 ILE cc_start: 0.8294 (mt) cc_final: 0.7950 (pt) REVERT: C 121 MET cc_start: 0.8046 (mmt) cc_final: 0.7745 (mmt) outliers start: 29 outliers final: 20 residues processed: 183 average time/residue: 0.0841 time to fit residues: 22.6012 Evaluate side-chains 187 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 419 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 0.0670 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.190365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140986 restraints weight = 9859.787| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.40 r_work: 0.3154 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9636 Z= 0.177 Angle : 0.644 11.021 13092 Z= 0.315 Chirality : 0.042 0.167 1659 Planarity : 0.004 0.030 1572 Dihedral : 7.522 68.913 1527 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.44 % Allowed : 21.63 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.25), residues: 1227 helix: 0.91 (0.18), residues: 921 sheet: -2.18 (0.84), residues: 30 loop : -1.36 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 173 TYR 0.015 0.001 TYR B 336 PHE 0.011 0.001 PHE A 249 TRP 0.010 0.002 TRP A 472 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9636) covalent geometry : angle 0.64392 (13092) hydrogen bonds : bond 0.03749 ( 648) hydrogen bonds : angle 4.55412 ( 1917) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.7124 (mmt) cc_final: 0.5725 (ptm) REVERT: A 325 ILE cc_start: 0.8688 (mm) cc_final: 0.8460 (mm) REVERT: A 467 LEU cc_start: 0.6468 (mp) cc_final: 0.6146 (mt) REVERT: A 477 MET cc_start: 0.6847 (mmt) cc_final: 0.6611 (mmt) REVERT: A 498 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6960 (mtmm) REVERT: B 73 ASP cc_start: 0.7782 (p0) cc_final: 0.7468 (p0) REVERT: B 125 MET cc_start: 0.6679 (mmt) cc_final: 0.5676 (ptm) REVERT: B 265 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7078 (tt) REVERT: B 311 ARG cc_start: 0.6745 (ttm170) cc_final: 0.5880 (ttt180) REVERT: C 125 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.5611 (ptm) REVERT: C 265 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7120 (tt) REVERT: C 415 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7598 (tpt) outliers start: 35 outliers final: 26 residues processed: 204 average time/residue: 0.0857 time to fit residues: 25.5901 Evaluate side-chains 209 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 73 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.194625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145929 restraints weight = 9698.362| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.17 r_work: 0.3216 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9636 Z= 0.126 Angle : 0.597 11.887 13092 Z= 0.294 Chirality : 0.040 0.190 1659 Planarity : 0.003 0.031 1572 Dihedral : 7.365 69.368 1527 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.15 % Allowed : 21.73 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1227 helix: 1.13 (0.18), residues: 918 sheet: -2.07 (0.85), residues: 30 loop : -1.39 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 87 TYR 0.016 0.001 TYR B 494 PHE 0.012 0.001 PHE B 185 TRP 0.009 0.001 TRP A 472 HIS 0.012 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9636) covalent geometry : angle 0.59736 (13092) hydrogen bonds : bond 0.03362 ( 648) hydrogen bonds : angle 4.38634 ( 1917) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8018 (mt) cc_final: 0.7721 (mt) REVERT: A 125 MET cc_start: 0.6897 (mmt) cc_final: 0.5808 (ptm) REVERT: A 325 ILE cc_start: 0.8678 (mm) cc_final: 0.8438 (mm) REVERT: A 498 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7248 (mtmm) REVERT: B 125 MET cc_start: 0.6472 (mmt) cc_final: 0.5742 (ptm) REVERT: B 311 ARG cc_start: 0.6866 (ttm170) cc_final: 0.6011 (ttt180) REVERT: B 398 MET cc_start: 0.7045 (mtp) cc_final: 0.6768 (mtt) REVERT: C 125 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.5638 (ptm) REVERT: C 467 LEU cc_start: 0.6596 (mp) cc_final: 0.6200 (mt) REVERT: C 477 MET cc_start: 0.7347 (mmp) cc_final: 0.6814 (mmm) outliers start: 32 outliers final: 26 residues processed: 192 average time/residue: 0.0876 time to fit residues: 24.4444 Evaluate side-chains 197 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 428 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.196297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145180 restraints weight = 9742.224| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.01 r_work: 0.3232 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9636 Z= 0.133 Angle : 0.619 12.833 13092 Z= 0.302 Chirality : 0.041 0.175 1659 Planarity : 0.004 0.039 1572 Dihedral : 7.276 67.691 1527 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.44 % Allowed : 21.63 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.25), residues: 1227 helix: 1.16 (0.18), residues: 930 sheet: -2.11 (0.83), residues: 30 loop : -1.48 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 478 TYR 0.018 0.001 TYR B 336 PHE 0.011 0.001 PHE B 185 TRP 0.009 0.001 TRP A 472 HIS 0.007 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9636) covalent geometry : angle 0.61930 (13092) hydrogen bonds : bond 0.03386 ( 648) hydrogen bonds : angle 4.39450 ( 1917) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6939 (mmt) cc_final: 0.5787 (ptm) REVERT: A 325 ILE cc_start: 0.8636 (mm) cc_final: 0.8411 (mm) REVERT: A 498 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7175 (mtmm) REVERT: B 125 MET cc_start: 0.6604 (mmt) cc_final: 0.5713 (ptm) REVERT: B 311 ARG cc_start: 0.6671 (ttm170) cc_final: 0.5888 (ttt180) REVERT: B 398 MET cc_start: 0.7127 (mtp) cc_final: 0.6879 (mtt) REVERT: B 477 MET cc_start: 0.7614 (mmp) cc_final: 0.7280 (mmm) REVERT: C 125 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.5512 (ptm) REVERT: C 265 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6881 (tt) REVERT: C 312 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7681 (pt0) REVERT: C 467 LEU cc_start: 0.6194 (mp) cc_final: 0.5756 (mt) outliers start: 35 outliers final: 27 residues processed: 189 average time/residue: 0.0829 time to fit residues: 22.8676 Evaluate side-chains 198 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 312 GLN Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.200550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.151686 restraints weight = 9546.003| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.69 r_work: 0.3405 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9636 Z= 0.121 Angle : 0.609 13.798 13092 Z= 0.296 Chirality : 0.040 0.266 1659 Planarity : 0.003 0.042 1572 Dihedral : 7.165 70.525 1527 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.95 % Allowed : 22.03 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.25), residues: 1227 helix: 1.35 (0.18), residues: 918 sheet: -2.13 (0.83), residues: 30 loop : -1.38 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 87 TYR 0.018 0.001 TYR B 494 PHE 0.009 0.001 PHE A 252 TRP 0.008 0.001 TRP A 472 HIS 0.008 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9636) covalent geometry : angle 0.60916 (13092) hydrogen bonds : bond 0.03285 ( 648) hydrogen bonds : angle 4.32516 ( 1917) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6651 (mmt) cc_final: 0.5732 (ptm) REVERT: A 498 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7318 (mtmm) REVERT: B 125 MET cc_start: 0.6318 (mmt) cc_final: 0.5781 (ptm) REVERT: B 179 ASN cc_start: 0.6803 (t0) cc_final: 0.6228 (t0) REVERT: B 311 ARG cc_start: 0.6819 (ttm170) cc_final: 0.5985 (ttt180) REVERT: B 398 MET cc_start: 0.7039 (mtp) cc_final: 0.6794 (mtt) REVERT: B 477 MET cc_start: 0.7736 (mmp) cc_final: 0.7388 (mmm) REVERT: C 125 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.5608 (ptm) REVERT: C 265 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6733 (tt) REVERT: C 477 MET cc_start: 0.7467 (mmp) cc_final: 0.6880 (mmm) outliers start: 30 outliers final: 26 residues processed: 189 average time/residue: 0.0838 time to fit residues: 22.9312 Evaluate side-chains 200 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 106 optimal weight: 0.0050 chunk 34 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.201071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.152462 restraints weight = 9408.785| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.73 r_work: 0.3311 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9636 Z= 0.126 Angle : 0.627 14.145 13092 Z= 0.304 Chirality : 0.041 0.254 1659 Planarity : 0.004 0.043 1572 Dihedral : 7.161 66.586 1527 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.15 % Allowed : 22.32 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.25), residues: 1227 helix: 1.31 (0.18), residues: 930 sheet: -2.12 (0.83), residues: 30 loop : -1.43 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 478 TYR 0.019 0.001 TYR B 336 PHE 0.010 0.001 PHE B 269 TRP 0.008 0.001 TRP A 472 HIS 0.007 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9636) covalent geometry : angle 0.62746 (13092) hydrogen bonds : bond 0.03333 ( 648) hydrogen bonds : angle 4.32573 ( 1917) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6647 (mmt) cc_final: 0.5762 (ptm) REVERT: A 498 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7105 (mtmm) REVERT: B 125 MET cc_start: 0.6271 (mmt) cc_final: 0.5796 (ptm) REVERT: B 179 ASN cc_start: 0.6819 (t0) cc_final: 0.6300 (t0) REVERT: B 311 ARG cc_start: 0.6893 (ttm170) cc_final: 0.5924 (ttt180) REVERT: B 398 MET cc_start: 0.7044 (mtp) cc_final: 0.6814 (mtt) REVERT: B 477 MET cc_start: 0.7885 (mmp) cc_final: 0.7544 (mmm) REVERT: C 125 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5644 (ptm) REVERT: C 265 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6735 (tt) REVERT: C 477 MET cc_start: 0.7474 (mmp) cc_final: 0.6931 (mmm) outliers start: 32 outliers final: 29 residues processed: 190 average time/residue: 0.0801 time to fit residues: 22.3654 Evaluate side-chains 204 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 84 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.199382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149966 restraints weight = 9382.631| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.76 r_work: 0.3300 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9636 Z= 0.130 Angle : 0.626 13.987 13092 Z= 0.305 Chirality : 0.041 0.268 1659 Planarity : 0.004 0.045 1572 Dihedral : 7.085 65.662 1527 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.24 % Allowed : 22.81 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.24), residues: 1227 helix: 1.42 (0.18), residues: 921 sheet: -2.14 (0.82), residues: 30 loop : -1.51 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 173 TYR 0.008 0.001 TYR B 336 PHE 0.015 0.001 PHE B 185 TRP 0.008 0.001 TRP A 472 HIS 0.008 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9636) covalent geometry : angle 0.62560 (13092) hydrogen bonds : bond 0.03351 ( 648) hydrogen bonds : angle 4.33907 ( 1917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2667.19 seconds wall clock time: 46 minutes 18.72 seconds (2778.72 seconds total)