Starting phenix.real_space_refine on Sun Jun 8 07:34:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvw_61845/06_2025/9jvw_61845.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvw_61845/06_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_61845/06_2025/9jvw_61845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvw_61845/06_2025/9jvw_61845.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvw_61845/06_2025/9jvw_61845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvw_61845/06_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-5710/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: 5.64, per 1000 atoms: 0.59 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 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: 0.86 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: 2.66 Time building geometry restraints manager: 2.79 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: 0.07 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.330 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- 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 : 0.943 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: 0.2153 time to fit residues: 80.9897 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 : 0.942 ------------------------------------------------------------------------------- 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: 0.0060 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: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 271 ASN A 327 HIS B 327 HIS ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 327 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.194888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.148461 restraints weight = 9725.558| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.88 r_work: 0.3309 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9636 Z= 0.122 Angle : 0.617 9.396 13092 Z= 0.307 Chirality : 0.040 0.143 1659 Planarity : 0.004 0.038 1572 Dihedral : 10.023 80.749 1527 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.16 % Allowed : 14.85 % Favored : 82.99 % 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: -1.49 (0.23), residues: 1227 helix: -0.43 (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 0.012 0.001 TRP B 472 HIS 0.010 0.002 HIS C 71 PHE 0.019 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 0.03813 ( 648) hydrogen bonds : angle 4.81867 ( 1917) covalent geometry : bond 0.00249 ( 9636) covalent geometry : angle 0.61673 (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 220 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7937 (t0) cc_final: 0.7664 (t0) REVERT: A 121 MET cc_start: 0.7892 (mmm) cc_final: 0.7668 (mmm) REVERT: A 125 MET cc_start: 0.7104 (mmt) cc_final: 0.5905 (ptm) REVERT: A 173 ARG cc_start: 0.7022 (mtt180) cc_final: 0.6640 (mtt-85) REVERT: A 325 ILE cc_start: 0.8650 (mm) cc_final: 0.8442 (mm) REVERT: A 478 ARG cc_start: 0.8361 (mtm180) cc_final: 0.8158 (mtm180) REVERT: B 98 ILE cc_start: 0.8050 (mt) cc_final: 0.7821 (pt) REVERT: B 125 MET cc_start: 0.6441 (mmt) cc_final: 0.5802 (ptm) REVERT: B 259 MET cc_start: 0.6239 (mtt) cc_final: 0.6037 (mtm) REVERT: B 315 MET cc_start: 0.6580 (mmt) cc_final: 0.6336 (tpp) REVERT: B 336 TYR cc_start: 0.7804 (t80) cc_final: 0.7560 (t80) REVERT: B 498 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6741 (mtmm) REVERT: C 98 ILE cc_start: 0.8261 (mt) cc_final: 0.7974 (pt) REVERT: C 125 MET cc_start: 0.7217 (mmt) cc_final: 0.5754 (ttp) REVERT: C 234 LEU cc_start: 0.7398 (mt) cc_final: 0.7178 (mp) REVERT: C 498 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7138 (mtmm) outliers start: 22 outliers final: 16 residues processed: 212 average time/residue: 0.1884 time to fit residues: 58.0577 Evaluate side-chains 192 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain 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 498 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 20 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.191519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145743 restraints weight = 9793.902| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.22 r_work: 0.3171 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9636 Z= 0.153 Angle : 0.626 8.356 13092 Z= 0.312 Chirality : 0.041 0.144 1659 Planarity : 0.004 0.037 1572 Dihedral : 8.210 76.792 1527 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.54 % Allowed : 18.29 % Favored : 78.17 % 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: 0.18 (0.18), residues: 927 sheet: -2.13 (0.86), residues: 30 loop : -1.76 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 472 HIS 0.008 0.001 HIS C 71 PHE 0.015 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 0.03848 ( 648) hydrogen bonds : angle 4.66033 ( 1917) covalent geometry : bond 0.00358 ( 9636) covalent geometry : angle 0.62578 (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 224 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7956 (t0) cc_final: 0.7634 (t0) REVERT: A 125 MET cc_start: 0.7017 (mmt) cc_final: 0.5906 (ptt) REVERT: A 325 ILE cc_start: 0.8679 (mm) cc_final: 0.8435 (mm) REVERT: A 387 ARG cc_start: 0.7309 (mmt180) cc_final: 0.6942 (mpt180) REVERT: B 98 ILE cc_start: 0.8215 (mt) cc_final: 0.7872 (pt) REVERT: B 125 MET cc_start: 0.6414 (mmt) cc_final: 0.5678 (ptm) REVERT: B 266 MET cc_start: 0.5921 (ttt) cc_final: 0.5709 (ttt) REVERT: B 311 ARG cc_start: 0.6858 (ttm170) cc_final: 0.5989 (ttt90) REVERT: B 315 MET cc_start: 0.6649 (mmt) cc_final: 0.6408 (tpp) REVERT: B 498 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6835 (mtmm) REVERT: C 98 ILE cc_start: 0.8386 (mt) cc_final: 0.7913 (pt) REVERT: C 125 MET cc_start: 0.6976 (mmt) cc_final: 0.5838 (ptm) REVERT: C 498 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7126 (mtmm) outliers start: 36 outliers final: 27 residues processed: 210 average time/residue: 0.1980 time to fit residues: 59.5681 Evaluate side-chains 202 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 392 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 420 LEU 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 60 CYS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 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: 0.6980 chunk 82 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 3 optimal weight: 0.0070 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.189627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140964 restraints weight = 9668.383| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.26 r_work: 0.3251 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9636 Z= 0.137 Angle : 0.601 8.552 13092 Z= 0.296 Chirality : 0.040 0.154 1659 Planarity : 0.004 0.032 1572 Dihedral : 7.706 73.546 1527 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.44 % Allowed : 20.65 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1227 helix: 0.56 (0.18), residues: 927 sheet: -2.16 (0.85), residues: 30 loop : -1.60 (0.35), residues: 270 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 0.013 0.001 PHE B 252 TYR 0.013 0.001 TYR C 494 ARG 0.002 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 648) hydrogen bonds : angle 4.52578 ( 1917) covalent geometry : bond 0.00320 ( 9636) covalent geometry : angle 0.60113 (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 218 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.7046 (mmt) cc_final: 0.5811 (ptt) REVERT: A 325 ILE cc_start: 0.8712 (mm) cc_final: 0.8469 (mm) REVERT: B 125 MET cc_start: 0.6630 (mmt) cc_final: 0.5746 (ptm) REVERT: B 266 MET cc_start: 0.6147 (ttt) cc_final: 0.5880 (ttt) REVERT: B 311 ARG cc_start: 0.6761 (ttm170) cc_final: 0.5948 (ttt90) REVERT: B 315 MET cc_start: 0.6523 (mmt) cc_final: 0.6315 (tpp) REVERT: B 387 ARG cc_start: 0.7706 (mpt180) cc_final: 0.7433 (mmt180) REVERT: B 498 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6735 (mtmm) REVERT: C 125 MET cc_start: 0.7039 (mmt) cc_final: 0.5892 (ptm) REVERT: C 265 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7120 (tt) outliers start: 35 outliers final: 27 residues processed: 201 average time/residue: 0.1933 time to fit residues: 55.8418 Evaluate side-chains 199 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 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 48 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 428 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 81 optimal weight: 0.0970 chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 27 optimal weight: 0.0060 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.194383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144498 restraints weight = 9648.568| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.98 r_work: 0.3355 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9636 Z= 0.106 Angle : 0.561 9.161 13092 Z= 0.277 Chirality : 0.039 0.153 1659 Planarity : 0.003 0.030 1572 Dihedral : 7.398 73.312 1527 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.75 % Allowed : 21.53 % 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: 0.53 (0.25), residues: 1227 helix: 1.04 (0.18), residues: 915 sheet: -1.91 (0.85), residues: 30 loop : -1.55 (0.34), residues: 282 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 0.011 0.001 PHE B 252 TYR 0.014 0.001 TYR C 494 ARG 0.004 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 648) hydrogen bonds : angle 4.29944 ( 1917) covalent geometry : bond 0.00226 ( 9636) covalent geometry : angle 0.56097 (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 203 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6643 (mmt) cc_final: 0.5794 (ptm) REVERT: A 325 ILE cc_start: 0.8692 (mm) cc_final: 0.8441 (mm) REVERT: A 467 LEU cc_start: 0.6355 (mp) cc_final: 0.6150 (mt) REVERT: A 477 MET cc_start: 0.6930 (mmt) cc_final: 0.6689 (mmt) REVERT: A 498 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6960 (mtmm) REVERT: B 125 MET cc_start: 0.6260 (mmt) cc_final: 0.5808 (ptm) REVERT: B 258 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7526 (ttmt) REVERT: B 336 TYR cc_start: 0.7846 (t80) cc_final: 0.7642 (t80) REVERT: B 398 MET cc_start: 0.6705 (mmm) cc_final: 0.6474 (mmm) REVERT: B 498 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6779 (mtmm) outliers start: 28 outliers final: 20 residues processed: 188 average time/residue: 0.1955 time to fit residues: 53.3037 Evaluate side-chains 185 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 93 ILE 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 258 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 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 367 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 428 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.192630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143628 restraints weight = 9728.794| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.24 r_work: 0.3183 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9636 Z= 0.131 Angle : 0.599 10.966 13092 Z= 0.292 Chirality : 0.040 0.170 1659 Planarity : 0.003 0.028 1572 Dihedral : 7.370 70.981 1527 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.15 % Allowed : 21.93 % 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: 0.64 (0.25), residues: 1227 helix: 1.07 (0.18), residues: 921 sheet: -2.08 (0.83), residues: 30 loop : -1.34 (0.35), residues: 276 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 A 249 TYR 0.015 0.001 TYR C 494 ARG 0.003 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 648) hydrogen bonds : angle 4.36869 ( 1917) covalent geometry : bond 0.00304 ( 9636) covalent geometry : angle 0.59915 (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 207 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6813 (mmt) cc_final: 0.5869 (ptm) REVERT: A 325 ILE cc_start: 0.8705 (mm) cc_final: 0.8462 (mm) REVERT: A 467 LEU cc_start: 0.6370 (mp) cc_final: 0.6029 (mt) REVERT: A 477 MET cc_start: 0.6849 (mmt) cc_final: 0.6618 (mmt) REVERT: A 498 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7034 (mtmm) REVERT: B 125 MET cc_start: 0.6401 (mmt) cc_final: 0.5837 (ptm) REVERT: B 258 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7616 (ttmt) REVERT: B 311 ARG cc_start: 0.6872 (ttm170) cc_final: 0.6007 (ttt180) outliers start: 32 outliers final: 25 residues processed: 193 average time/residue: 0.2089 time to fit residues: 58.3546 Evaluate side-chains 203 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 258 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 415 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 94 optimal weight: 0.0270 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.195887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.147353 restraints weight = 9598.027| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.01 r_work: 0.3259 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9636 Z= 0.115 Angle : 0.583 11.639 13092 Z= 0.286 Chirality : 0.040 0.211 1659 Planarity : 0.003 0.028 1572 Dihedral : 7.236 70.046 1527 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.44 % Allowed : 22.12 % Favored : 74.43 % 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: 0.85 (0.25), residues: 1227 helix: 1.25 (0.18), residues: 918 sheet: -2.06 (0.83), residues: 30 loop : -1.32 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.003 0.001 HIS A 71 PHE 0.009 0.001 PHE B 252 TYR 0.019 0.001 TYR B 336 ARG 0.002 0.000 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 648) hydrogen bonds : angle 4.27851 ( 1917) covalent geometry : bond 0.00256 ( 9636) covalent geometry : angle 0.58261 (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 204 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6673 (mmt) cc_final: 0.5903 (ptm) REVERT: A 325 ILE cc_start: 0.8582 (mm) cc_final: 0.8364 (mm) REVERT: A 477 MET cc_start: 0.6923 (mmt) cc_final: 0.6661 (mmt) REVERT: A 498 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7242 (mtmm) REVERT: B 78 ILE cc_start: 0.7945 (tt) cc_final: 0.7718 (pt) REVERT: B 125 MET cc_start: 0.6271 (mmt) cc_final: 0.5884 (ptm) REVERT: B 311 ARG cc_start: 0.6994 (ttm170) cc_final: 0.6054 (ttt180) REVERT: B 477 MET cc_start: 0.7779 (mmp) cc_final: 0.7387 (mmm) REVERT: B 498 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6991 (mtmm) REVERT: C 265 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6778 (tt) REVERT: C 477 MET cc_start: 0.7425 (mmp) cc_final: 0.6862 (mmm) outliers start: 35 outliers final: 24 residues processed: 188 average time/residue: 0.1822 time to fit residues: 49.3004 Evaluate side-chains 192 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 415 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 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 498 LYS Chi-restraints excluded: chain C residue 60 CYS 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 415 MET 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: 0.9990 chunk 51 optimal weight: 0.3980 chunk 96 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.198029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.148684 restraints weight = 9635.430| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.94 r_work: 0.3313 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9636 Z= 0.107 Angle : 0.584 12.644 13092 Z= 0.284 Chirality : 0.039 0.229 1659 Planarity : 0.003 0.033 1572 Dihedral : 7.089 69.265 1527 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.05 % Allowed : 22.12 % Favored : 74.83 % 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: 1.09 (0.25), residues: 1227 helix: 1.49 (0.18), residues: 909 sheet: -2.01 (0.83), residues: 30 loop : -1.40 (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 A 71 PHE 0.010 0.001 PHE B 269 TYR 0.018 0.001 TYR B 494 ARG 0.002 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.03032 ( 648) hydrogen bonds : angle 4.18138 ( 1917) covalent geometry : bond 0.00232 ( 9636) covalent geometry : angle 0.58351 (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 206 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6546 (mmt) cc_final: 0.5829 (ptm) REVERT: A 325 ILE cc_start: 0.8517 (mm) cc_final: 0.8270 (mm) REVERT: A 498 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7138 (mtmm) REVERT: B 125 MET cc_start: 0.6053 (mmt) cc_final: 0.4865 (mmt) REVERT: B 258 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7539 (ttmt) REVERT: B 498 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6967 (mtmm) REVERT: C 264 LYS cc_start: 0.6593 (tttm) cc_final: 0.6391 (tppt) REVERT: C 265 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6681 (tt) REVERT: C 477 MET cc_start: 0.7368 (mmp) cc_final: 0.6829 (mmm) outliers start: 31 outliers final: 23 residues processed: 190 average time/residue: 0.1921 time to fit residues: 52.5696 Evaluate side-chains 199 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 415 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 258 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 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 60 CYS 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 415 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 428 VAL 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: 0.2980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 32 optimal weight: 0.2980 chunk 48 optimal weight: 20.0000 chunk 16 optimal weight: 0.0170 chunk 85 optimal weight: 0.0020 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.2626 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.201892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.153266 restraints weight = 9455.341| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.85 r_work: 0.3326 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9636 Z= 0.103 Angle : 0.580 13.024 13092 Z= 0.283 Chirality : 0.039 0.198 1659 Planarity : 0.003 0.035 1572 Dihedral : 6.924 68.429 1527 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.56 % Allowed : 22.81 % Favored : 74.63 % 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: 1.64 (0.18), residues: 909 sheet: -1.62 (0.87), residues: 30 loop : -1.39 (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 0.014 0.001 TYR B 336 ARG 0.002 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.02910 ( 648) hydrogen bonds : angle 4.08014 ( 1917) covalent geometry : bond 0.00218 ( 9636) covalent geometry : angle 0.58039 (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 210 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.7919 (mt) cc_final: 0.7656 (mm) REVERT: A 125 MET cc_start: 0.6283 (mmt) cc_final: 0.6080 (ptm) REVERT: A 498 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7079 (mtmm) REVERT: B 121 MET cc_start: 0.7842 (mmm) cc_final: 0.6807 (mmm) REVERT: B 258 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7514 (ttmt) REVERT: B 477 MET cc_start: 0.7671 (mmp) cc_final: 0.7207 (mmm) REVERT: B 498 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7024 (mtmm) REVERT: C 477 MET cc_start: 0.7458 (mmp) cc_final: 0.6874 (mmm) outliers start: 26 outliers final: 20 residues processed: 196 average time/residue: 0.1901 time to fit residues: 53.9074 Evaluate side-chains 195 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 415 MET 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 258 LYS 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 429 SER Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 428 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: 4.9990 chunk 85 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.199369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.148767 restraints weight = 9490.537| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.74 r_work: 0.3410 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9636 Z= 0.151 Angle : 0.670 13.927 13092 Z= 0.321 Chirality : 0.042 0.308 1659 Planarity : 0.004 0.036 1572 Dihedral : 7.005 63.668 1527 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.36 % Allowed : 23.60 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1227 helix: 1.53 (0.18), residues: 909 sheet: -2.12 (0.81), residues: 30 loop : -1.35 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 286 HIS 0.003 0.001 HIS A 71 PHE 0.011 0.001 PHE C 80 TYR 0.019 0.001 TYR B 494 ARG 0.003 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 648) hydrogen bonds : angle 4.29850 ( 1917) covalent geometry : bond 0.00366 ( 9636) covalent geometry : angle 0.66966 (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 199 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6464 (mmt) cc_final: 0.5870 (ptm) REVERT: A 498 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7135 (mtmm) REVERT: B 258 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7616 (ttmt) REVERT: B 311 ARG cc_start: 0.6761 (ttm170) cc_final: 0.5929 (ttt180) REVERT: B 477 MET cc_start: 0.7879 (mmp) cc_final: 0.7548 (mmm) REVERT: C 265 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6922 (tt) REVERT: C 477 MET cc_start: 0.7467 (mmp) cc_final: 0.6928 (mmm) outliers start: 24 outliers final: 21 residues processed: 187 average time/residue: 0.2227 time to fit residues: 60.8300 Evaluate side-chains 195 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 415 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain B residue 258 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 415 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain C residue 60 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 121 optimal weight: 0.8980 chunk 17 optimal weight: 0.0170 chunk 47 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.201731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151745 restraints weight = 9469.532| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.76 r_work: 0.3397 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9636 Z= 0.109 Angle : 0.607 13.665 13092 Z= 0.294 Chirality : 0.040 0.306 1659 Planarity : 0.003 0.041 1572 Dihedral : 6.863 65.527 1527 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.46 % Allowed : 23.50 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1227 helix: 1.75 (0.18), residues: 909 sheet: -1.77 (0.84), residues: 30 loop : -1.39 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 472 HIS 0.003 0.001 HIS A 71 PHE 0.014 0.001 PHE B 185 TYR 0.012 0.001 TYR B 336 ARG 0.002 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 648) hydrogen bonds : angle 4.09006 ( 1917) covalent geometry : bond 0.00235 ( 9636) covalent geometry : angle 0.60653 (13092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5473.81 seconds wall clock time: 94 minutes 49.69 seconds (5689.69 seconds total)