Starting phenix.real_space_refine on Mon May 12 21:39:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvw_61845/05_2025/9jvw_61845.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvw_61845/05_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_61845/05_2025/9jvw_61845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvw_61845/05_2025/9jvw_61845.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvw_61845/05_2025/9jvw_61845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvw_61845/05_2025/9jvw_61845.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.022 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.49, per 1000 atoms: 0.58 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: 2.51 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.93 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: 2.83 Time building geometry restraints manager: 2.85 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.730 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.520 ------------------------------------------------------------------------------- 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 : 7.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.002 TRP A 472 HIS 0.006 0.002 HIS A 495 PHE 0.020 0.002 PHE B 348 TYR 0.013 0.003 TYR B 316 ARG 0.002 0.000 ARG B 311 Details of bonding type rmsd hydrogen bonds : bond 0.17956 ( 648) hydrogen bonds : angle 7.19689 ( 1917) covalent geometry : bond 0.00804 ( 9636) covalent geometry : angle 1.11646 (13092) *********************** 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 : 1.063 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: 0.2070 time to fit residues: 78.1136 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 : 0.850 ------------------------------------------------------------------------------- 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 103 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 0.0980 chunk 37 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.194996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.151098 restraints weight = 9731.784| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.97 r_work: 0.3258 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9636 Z= 0.127 Angle : 0.626 8.923 13092 Z= 0.312 Chirality : 0.040 0.140 1659 Planarity : 0.004 0.039 1572 Dihedral : 9.964 80.482 1527 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.16 % Allowed : 14.65 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1227 helix: -0.46 (0.17), residues: 936 sheet: -3.05 (0.87), residues: 36 loop : -2.30 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 472 HIS 0.010 0.001 HIS C 71 PHE 0.020 0.001 PHE B 388 TYR 0.009 0.001 TYR A 316 ARG 0.004 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 648) hydrogen bonds : angle 4.81714 ( 1917) covalent geometry : bond 0.00258 ( 9636) covalent geometry : angle 0.62633 (13092) *********************** 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 219 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8013 (t0) cc_final: 0.7730 (t0) REVERT: A 86 MET cc_start: 0.7800 (mmt) cc_final: 0.7285 (mmt) REVERT: A 121 MET cc_start: 0.7896 (mmm) cc_final: 0.7659 (mmm) REVERT: A 125 MET cc_start: 0.7108 (mmt) cc_final: 0.5910 (ptm) REVERT: A 173 ARG cc_start: 0.7049 (mtt180) cc_final: 0.6674 (mtt-85) REVERT: A 325 ILE cc_start: 0.8627 (mm) cc_final: 0.8407 (mm) REVERT: B 98 ILE cc_start: 0.8066 (mt) cc_final: 0.7785 (pt) REVERT: B 125 MET cc_start: 0.6461 (mmt) cc_final: 0.5805 (ptm) REVERT: B 315 MET cc_start: 0.6545 (mmt) cc_final: 0.6298 (tpp) REVERT: B 336 TYR cc_start: 0.7806 (t80) cc_final: 0.7552 (t80) REVERT: B 387 ARG cc_start: 0.7686 (mpt180) cc_final: 0.7422 (mmt180) REVERT: B 498 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6871 (mtmm) REVERT: C 98 ILE cc_start: 0.8272 (mt) cc_final: 0.7934 (pt) REVERT: C 121 MET cc_start: 0.8054 (mmt) cc_final: 0.7822 (mmt) REVERT: C 125 MET cc_start: 0.7227 (mmt) cc_final: 0.5788 (ttp) REVERT: C 234 LEU cc_start: 0.7397 (mt) cc_final: 0.7174 (mp) REVERT: C 498 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7076 (mtmm) outliers start: 22 outliers final: 16 residues processed: 213 average time/residue: 0.1800 time to fit residues: 56.1298 Evaluate side-chains 189 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 419 VAL 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 419 VAL 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 449 THR 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 20 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 94 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.191487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142227 restraints weight = 9829.453| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.33 r_work: 0.3277 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9636 Z= 0.121 Angle : 0.584 8.448 13092 Z= 0.291 Chirality : 0.040 0.142 1659 Planarity : 0.004 0.037 1572 Dihedral : 8.235 77.015 1527 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.05 % Allowed : 18.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1227 helix: 0.24 (0.18), residues: 951 sheet: -2.97 (0.83), residues: 36 loop : -2.06 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 472 HIS 0.007 0.001 HIS C 71 PHE 0.012 0.001 PHE B 252 TYR 0.013 0.001 TYR C 336 ARG 0.002 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 648) hydrogen bonds : angle 4.54329 ( 1917) covalent geometry : bond 0.00264 ( 9636) covalent geometry : angle 0.58409 (13092) *********************** 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 213 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8086 (t0) cc_final: 0.7780 (t0) REVERT: A 125 MET cc_start: 0.6964 (mmt) cc_final: 0.5871 (ptt) REVERT: A 325 ILE cc_start: 0.8621 (mm) cc_final: 0.8370 (mm) REVERT: A 336 TYR cc_start: 0.7909 (t80) cc_final: 0.7693 (t80) REVERT: A 387 ARG cc_start: 0.7391 (mmt180) cc_final: 0.6989 (mpt180) REVERT: B 98 ILE cc_start: 0.8291 (mt) cc_final: 0.7897 (pt) REVERT: B 125 MET cc_start: 0.6451 (mmt) cc_final: 0.5728 (ptm) REVERT: B 305 ASP cc_start: 0.5998 (t0) cc_final: 0.5775 (t70) REVERT: B 387 ARG cc_start: 0.7707 (mpt180) cc_final: 0.7444 (mmt180) REVERT: B 397 ASN cc_start: 0.7946 (t0) cc_final: 0.7740 (t0) REVERT: B 498 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6747 (mtmm) REVERT: C 98 ILE cc_start: 0.8441 (mt) cc_final: 0.7846 (pt) REVERT: C 125 MET cc_start: 0.7368 (mmt) cc_final: 0.6058 (ptm) REVERT: C 463 ASP cc_start: 0.6304 (t70) cc_final: 0.5941 (t70) REVERT: C 498 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7324 (mtmm) outliers start: 31 outliers final: 22 residues processed: 202 average time/residue: 0.1888 time to fit residues: 54.6649 Evaluate side-chains 192 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL 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 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 93 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 392 VAL 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 36 optimal weight: 0.5980 chunk 82 optimal weight: 10.9990 chunk 40 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 chunk 67 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** B 424 GLN C 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.195213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145210 restraints weight = 9555.815| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.80 r_work: 0.3241 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3521 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= 0.122 Angle : 0.583 8.436 13092 Z= 0.287 Chirality : 0.040 0.147 1659 Planarity : 0.003 0.033 1572 Dihedral : 7.583 73.869 1527 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.24 % Allowed : 20.45 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1227 helix: 0.59 (0.18), residues: 948 sheet: -2.05 (0.85), residues: 30 loop : -1.88 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.004 0.001 HIS C 71 PHE 0.011 0.001 PHE B 252 TYR 0.013 0.001 TYR C 494 ARG 0.004 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 648) hydrogen bonds : angle 4.46053 ( 1917) covalent geometry : bond 0.00274 ( 9636) covalent geometry : angle 0.58335 (13092) *********************** 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 204 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6819 (mmt) cc_final: 0.5888 (ptt) REVERT: A 325 ILE cc_start: 0.8698 (mm) cc_final: 0.8409 (mm) REVERT: A 467 LEU cc_start: 0.6393 (mp) cc_final: 0.6150 (mt) REVERT: B 98 ILE cc_start: 0.8228 (mt) cc_final: 0.7918 (pt) REVERT: B 125 MET cc_start: 0.6265 (mmt) cc_final: 0.5812 (ptm) REVERT: B 336 TYR cc_start: 0.7815 (t80) cc_final: 0.7573 (t80) REVERT: B 387 ARG cc_start: 0.7651 (mpt180) cc_final: 0.7373 (mmt180) REVERT: B 498 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6787 (mtmm) REVERT: C 98 ILE cc_start: 0.8393 (mt) cc_final: 0.7932 (pt) REVERT: C 498 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7180 (mtmm) outliers start: 33 outliers final: 23 residues processed: 188 average time/residue: 0.1867 time to fit residues: 51.0966 Evaluate side-chains 189 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER 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 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 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 498 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.195645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.146705 restraints weight = 9575.029| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.90 r_work: 0.3233 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9636 Z= 0.124 Angle : 0.580 9.561 13092 Z= 0.285 Chirality : 0.040 0.151 1659 Planarity : 0.003 0.030 1572 Dihedral : 7.342 72.720 1527 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.24 % Allowed : 20.35 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1227 helix: 1.01 (0.18), residues: 912 sheet: -1.89 (0.86), residues: 30 loop : -1.48 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.003 0.001 HIS C 71 PHE 0.010 0.001 PHE A 249 TYR 0.014 0.001 TYR C 494 ARG 0.002 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 648) hydrogen bonds : angle 4.36554 ( 1917) covalent geometry : bond 0.00283 ( 9636) covalent geometry : angle 0.57981 (13092) *********************** 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 201 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6715 (mmt) cc_final: 0.5828 (ptm) REVERT: A 325 ILE cc_start: 0.8720 (mm) cc_final: 0.8468 (mm) REVERT: A 467 LEU cc_start: 0.6449 (mp) cc_final: 0.6230 (mt) REVERT: A 498 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6948 (mtmm) REVERT: B 125 MET cc_start: 0.6215 (mmt) cc_final: 0.5853 (ptm) REVERT: B 311 ARG cc_start: 0.6940 (ttm170) cc_final: 0.6008 (ttt90) REVERT: B 387 ARG cc_start: 0.7705 (mpt180) cc_final: 0.7271 (mmt180) REVERT: B 498 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6790 (mtmm) REVERT: C 447 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7660 (tp) outliers start: 33 outliers final: 23 residues processed: 186 average time/residue: 0.1847 time to fit residues: 49.4071 Evaluate side-chains 186 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 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 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 B residue 447 LEU Chi-restraints excluded: chain B residue 498 LYS 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 447 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.194946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145833 restraints weight = 9586.100| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.04 r_work: 0.3212 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9636 Z= 0.116 Angle : 0.575 10.891 13092 Z= 0.282 Chirality : 0.039 0.175 1659 Planarity : 0.003 0.029 1572 Dihedral : 7.233 70.863 1527 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.44 % Allowed : 20.85 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1227 helix: 1.16 (0.18), residues: 918 sheet: -1.88 (0.87), residues: 30 loop : -1.36 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 472 HIS 0.005 0.001 HIS C 71 PHE 0.010 0.001 PHE B 269 TYR 0.016 0.001 TYR B 336 ARG 0.002 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 648) hydrogen bonds : angle 4.29986 ( 1917) covalent geometry : bond 0.00261 ( 9636) covalent geometry : angle 0.57501 (13092) *********************** 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 206 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.7005 (tpt) cc_final: 0.6693 (tpt) REVERT: A 125 MET cc_start: 0.6741 (mmt) cc_final: 0.5813 (ptm) REVERT: A 325 ILE cc_start: 0.8677 (mm) cc_final: 0.8418 (mm) REVERT: A 467 LEU cc_start: 0.6289 (mp) cc_final: 0.6080 (mt) REVERT: A 498 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6990 (mtmm) REVERT: B 78 ILE cc_start: 0.7903 (tt) cc_final: 0.7634 (pt) REVERT: B 125 MET cc_start: 0.6365 (mmt) cc_final: 0.5193 (mmt) REVERT: B 311 ARG cc_start: 0.6797 (ttm170) cc_final: 0.5873 (ttt90) REVERT: B 498 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.6934 (mtmm) REVERT: C 265 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6838 (tt) REVERT: C 467 LEU cc_start: 0.6316 (mp) cc_final: 0.6014 (mt) REVERT: C 497 SER cc_start: 0.8496 (m) cc_final: 0.8273 (p) outliers start: 35 outliers final: 24 residues processed: 188 average time/residue: 0.1794 time to fit residues: 48.4843 Evaluate side-chains 193 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 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 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 B residue 498 LYS 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 419 VAL Chi-restraints excluded: chain C residue 428 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 94 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.200744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.151518 restraints weight = 9501.176| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.78 r_work: 0.3276 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9636 Z= 0.122 Angle : 0.594 11.837 13092 Z= 0.289 Chirality : 0.040 0.249 1659 Planarity : 0.003 0.029 1572 Dihedral : 7.170 69.155 1527 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.44 % Allowed : 21.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1227 helix: 1.28 (0.18), residues: 918 sheet: -1.90 (0.86), residues: 30 loop : -1.29 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.002 0.001 HIS C 71 PHE 0.010 0.001 PHE B 269 TYR 0.017 0.001 TYR B 494 ARG 0.002 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 648) hydrogen bonds : angle 4.27896 ( 1917) covalent geometry : bond 0.00280 ( 9636) covalent geometry : angle 0.59417 (13092) *********************** 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 206 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6661 (mmt) cc_final: 0.5830 (ptm) REVERT: A 325 ILE cc_start: 0.8671 (mm) cc_final: 0.8458 (mm) REVERT: A 467 LEU cc_start: 0.6352 (mp) cc_final: 0.6133 (mt) REVERT: A 498 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7166 (mtmm) REVERT: B 77 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7266 (tt) REVERT: B 125 MET cc_start: 0.6318 (mmt) cc_final: 0.5152 (mmt) REVERT: B 311 ARG cc_start: 0.6905 (ttm170) cc_final: 0.5962 (ttt180) REVERT: B 477 MET cc_start: 0.7694 (mmp) cc_final: 0.7300 (mmm) REVERT: B 498 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.6981 (mtmm) REVERT: C 265 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6776 (tt) REVERT: C 477 MET cc_start: 0.7410 (mmp) cc_final: 0.6934 (mmm) outliers start: 35 outliers final: 25 residues processed: 190 average time/residue: 0.1777 time to fit residues: 49.1049 Evaluate side-chains 193 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 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 B residue 498 LYS Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 265 LEU 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 63 optimal weight: 4.9990 chunk 51 optimal weight: 0.0970 chunk 96 optimal weight: 0.0970 chunk 30 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 109 optimal weight: 0.0270 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.199594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.149595 restraints weight = 9682.687| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.79 r_work: 0.3324 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9636 Z= 0.103 Angle : 0.570 12.196 13092 Z= 0.277 Chirality : 0.038 0.166 1659 Planarity : 0.003 0.027 1572 Dihedral : 6.986 69.308 1527 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.65 % Allowed : 22.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1227 helix: 1.57 (0.18), residues: 909 sheet: -1.72 (0.86), residues: 30 loop : -1.42 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.003 0.001 HIS C 71 PHE 0.010 0.001 PHE B 269 TYR 0.018 0.001 TYR B 494 ARG 0.002 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.02916 ( 648) hydrogen bonds : angle 4.12679 ( 1917) covalent geometry : bond 0.00217 ( 9636) covalent geometry : angle 0.57022 (13092) *********************** 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 208 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6313 (mmt) cc_final: 0.5893 (ptm) REVERT: A 325 ILE cc_start: 0.8730 (mm) cc_final: 0.8479 (mm) REVERT: A 498 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7147 (mtmm) REVERT: B 77 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7249 (tt) REVERT: B 125 MET cc_start: 0.6243 (mmt) cc_final: 0.5190 (mmt) REVERT: B 264 LYS cc_start: 0.6572 (tttm) cc_final: 0.6371 (tppt) REVERT: B 477 MET cc_start: 0.7689 (mmp) cc_final: 0.7340 (mmm) REVERT: B 498 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7032 (mtmm) REVERT: C 265 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6606 (tt) REVERT: C 477 MET cc_start: 0.7438 (mmp) cc_final: 0.6932 (mmm) outliers start: 27 outliers final: 17 residues processed: 194 average time/residue: 0.1811 time to fit residues: 51.3501 Evaluate side-chains 189 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 498 LYS 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 415 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 419 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 97 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 32 optimal weight: 0.1980 chunk 48 optimal weight: 20.0000 chunk 16 optimal weight: 0.0570 chunk 85 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN C 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.203649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.155588 restraints weight = 9477.279| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.79 r_work: 0.3334 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 9636 Z= 0.110 Angle : 0.593 13.224 13092 Z= 0.289 Chirality : 0.039 0.234 1659 Planarity : 0.003 0.026 1572 Dihedral : 6.900 71.076 1527 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.46 % Allowed : 22.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1227 helix: 1.66 (0.18), residues: 909 sheet: -1.53 (0.87), residues: 30 loop : -1.49 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 472 HIS 0.003 0.001 HIS C 71 PHE 0.010 0.001 PHE B 269 TYR 0.006 0.001 TYR C 287 ARG 0.002 0.000 ARG B 478 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 648) hydrogen bonds : angle 4.11949 ( 1917) covalent geometry : bond 0.00247 ( 9636) covalent geometry : angle 0.59309 (13092) *********************** 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 193 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 ILE cc_start: 0.8746 (mm) cc_final: 0.8515 (mm) REVERT: A 498 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7081 (mtmm) REVERT: B 77 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7333 (tt) REVERT: B 98 ILE cc_start: 0.8119 (mt) cc_final: 0.7867 (pt) REVERT: B 125 MET cc_start: 0.6129 (mmt) cc_final: 0.5154 (mmt) REVERT: B 264 LYS cc_start: 0.6638 (tttm) cc_final: 0.6394 (tppt) REVERT: B 265 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6726 (tt) REVERT: B 477 MET cc_start: 0.7702 (mmp) cc_final: 0.7371 (mmm) REVERT: B 498 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7079 (mtmm) REVERT: C 265 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6655 (tt) REVERT: C 477 MET cc_start: 0.7559 (mmp) cc_final: 0.7026 (mmm) outliers start: 25 outliers final: 20 residues processed: 181 average time/residue: 0.1727 time to fit residues: 46.3061 Evaluate side-chains 186 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 389 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 385 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 498 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 82 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 85 optimal weight: 0.0270 chunk 7 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 0.0000 chunk 40 optimal weight: 5.9990 overall best weight: 0.9044 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.198897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150021 restraints weight = 9582.467| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.93 r_work: 0.3398 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9636 Z= 0.128 Angle : 0.626 13.765 13092 Z= 0.303 Chirality : 0.040 0.245 1659 Planarity : 0.004 0.033 1572 Dihedral : 6.925 68.406 1527 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.46 % Allowed : 23.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1227 helix: 1.66 (0.18), residues: 909 sheet: -1.83 (0.83), residues: 30 loop : -1.51 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.003 0.001 HIS C 71 PHE 0.010 0.001 PHE B 269 TYR 0.019 0.001 TYR B 494 ARG 0.002 0.000 ARG B 478 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 648) hydrogen bonds : angle 4.18964 ( 1917) covalent geometry : bond 0.00302 ( 9636) covalent geometry : angle 0.62618 (13092) ********************** 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 187 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.7132 (tpt) cc_final: 0.6810 (tpt) REVERT: A 325 ILE cc_start: 0.8755 (mm) cc_final: 0.8504 (mm) REVERT: A 498 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7120 (mtmm) REVERT: B 77 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7311 (tt) REVERT: B 125 MET cc_start: 0.6307 (mmt) cc_final: 0.5260 (mmt) REVERT: B 265 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6852 (tt) REVERT: B 477 MET cc_start: 0.7692 (mmp) cc_final: 0.7206 (mmm) REVERT: C 265 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6750 (tt) REVERT: C 477 MET cc_start: 0.7443 (mmp) cc_final: 0.6988 (mmm) outliers start: 25 outliers final: 19 residues processed: 175 average time/residue: 0.1696 time to fit residues: 43.4670 Evaluate side-chains 184 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 389 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 77 LEU 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 415 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 419 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 23 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.203915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.154559 restraints weight = 9497.892| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.74 r_work: 0.3432 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9636 Z= 0.116 Angle : 0.610 13.879 13092 Z= 0.296 Chirality : 0.041 0.311 1659 Planarity : 0.004 0.042 1572 Dihedral : 6.831 67.999 1527 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.06 % Allowed : 23.60 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1227 helix: 1.73 (0.18), residues: 909 sheet: -1.86 (0.83), residues: 30 loop : -1.53 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 472 HIS 0.003 0.001 HIS B 495 PHE 0.010 0.001 PHE B 269 TYR 0.005 0.001 TYR A 287 ARG 0.002 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 648) hydrogen bonds : angle 4.14306 ( 1917) covalent geometry : bond 0.00266 ( 9636) covalent geometry : angle 0.60981 (13092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5264.05 seconds wall clock time: 91 minutes 28.76 seconds (5488.76 seconds total)