Starting phenix.real_space_refine on Tue Aug 6 00:07:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/08_2024/8wy4_37915.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/08_2024/8wy4_37915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/08_2024/8wy4_37915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/08_2024/8wy4_37915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/08_2024/8wy4_37915.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/08_2024/8wy4_37915.cif" } resolution = 2.81 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= 0.001 sd= 0.031 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 48 5.16 5 C 9504 2.51 5 N 2448 2.21 5 O 2852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14864 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3685 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 8, 'TRANS': 442} Chain breaks: 1 Chain: "B" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3685 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 8, 'TRANS': 442} Chain breaks: 1 Chain: "D" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3685 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 8, 'TRANS': 442} Chain breaks: 1 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3685 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 8, 'TRANS': 442} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.28, per 1000 atoms: 0.62 Number of scatterers: 14864 At special positions: 0 Unit cell: (115.08, 190.68, 68.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 12 15.00 O 2852 8.00 N 2448 7.00 C 9504 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 - 3.50 Amino acid : False - 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.9 seconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 16 sheets defined 42.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.960A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 83 through 91 removed outlier: 3.860A pdb=" N LYS A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.612A pdb=" N LEU A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.784A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 removed outlier: 3.558A pdb=" N LYS A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.630A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 removed outlier: 4.019A pdb=" N CYS A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 493 Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.671A pdb=" N GLU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 528 removed outlier: 3.592A pdb=" N SER A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 528 " --> pdb=" O MET A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 540 removed outlier: 3.662A pdb=" N TYR A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.632A pdb=" N ASN A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 562 removed outlier: 3.564A pdb=" N CYS A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.960A pdb=" N LEU B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 83 through 91 removed outlier: 3.861A pdb=" N LYS B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.612A pdb=" N LEU B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR B 326 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 removed outlier: 3.784A pdb=" N SER B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 395 removed outlier: 3.558A pdb=" N LYS B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 413 through 423 removed outlier: 3.630A pdb=" N THR B 419 " --> pdb=" O HIS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 removed outlier: 4.019A pdb=" N CYS B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 Processing helix chain 'B' and resid 493 through 503 removed outlier: 3.671A pdb=" N GLU B 503 " --> pdb=" O GLU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 528 removed outlier: 3.592A pdb=" N SER B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 528 " --> pdb=" O MET B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.662A pdb=" N TYR B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER B 540 " --> pdb=" O TYR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.632A pdb=" N ASN B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 562 removed outlier: 3.564A pdb=" N CYS B 557 " --> pdb=" O SER B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 574 Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.960A pdb=" N LEU D 39 " --> pdb=" O LYS D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 83 through 91 removed outlier: 3.859A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 308 Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.612A pdb=" N LEU D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR D 326 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 370 removed outlier: 3.784A pdb=" N SER D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 395 removed outlier: 3.558A pdb=" N LYS D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 413 through 423 removed outlier: 3.629A pdb=" N THR D 419 " --> pdb=" O HIS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 457 removed outlier: 4.020A pdb=" N CYS D 453 " --> pdb=" O GLY D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 493 Processing helix chain 'D' and resid 493 through 503 removed outlier: 3.671A pdb=" N GLU D 503 " --> pdb=" O GLU D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 528 removed outlier: 3.592A pdb=" N SER D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 528 " --> pdb=" O MET D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 3.662A pdb=" N TYR D 536 " --> pdb=" O ASP D 532 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 551 removed outlier: 3.632A pdb=" N ASN D 544 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 562 removed outlier: 3.564A pdb=" N CYS D 557 " --> pdb=" O SER D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 574 Processing helix chain 'C' and resid 31 through 47 removed outlier: 3.959A pdb=" N LEU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 83 through 91 removed outlier: 3.860A pdb=" N LYS C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.612A pdb=" N LEU C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.784A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 removed outlier: 3.558A pdb=" N LYS C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 413 through 423 removed outlier: 3.630A pdb=" N THR C 419 " --> pdb=" O HIS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 457 removed outlier: 4.019A pdb=" N CYS C 453 " --> pdb=" O GLY C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 493 Processing helix chain 'C' and resid 493 through 503 removed outlier: 3.671A pdb=" N GLU C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 528 removed outlier: 3.592A pdb=" N SER C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 528 " --> pdb=" O MET C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 540 removed outlier: 3.662A pdb=" N TYR C 536 " --> pdb=" O ASP C 532 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 540 " --> pdb=" O TYR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 551 removed outlier: 3.633A pdb=" N ASN C 544 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 562 removed outlier: 3.565A pdb=" N CYS C 557 " --> pdb=" O SER C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 3.533A pdb=" N ILE A 8 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN A 5 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 127 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.726A pdb=" N VAL A 283 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407 removed outlier: 6.723A pdb=" N ARG A 374 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU A 406 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 376 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 20 removed outlier: 3.533A pdb=" N ILE B 8 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN B 5 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY B 127 " --> pdb=" O TYR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 removed outlier: 6.727A pdb=" N VAL B 283 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE B 316 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR B 285 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N SER B 318 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B 287 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 26 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL B 336 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE B 28 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.724A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AA9, first strand: chain 'D' and resid 17 through 20 removed outlier: 3.532A pdb=" N ILE D 8 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN D 5 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY D 127 " --> pdb=" O TYR D 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 149 through 154 removed outlier: 6.726A pdb=" N VAL D 283 " --> pdb=" O TYR D 314 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D 26 " --> pdb=" O ILE D 334 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL D 336 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE D 28 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 403 through 407 removed outlier: 6.723A pdb=" N ARG D 374 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU D 406 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU D 376 " --> pdb=" O LEU D 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 435 through 437 Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 20 removed outlier: 3.534A pdb=" N ILE C 8 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN C 5 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY C 127 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 154 removed outlier: 4.299A pdb=" N TYR C 314 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 403 through 407 removed outlier: 6.723A pdb=" N ARG C 374 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU C 406 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 376 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 435 through 437 600 hydrogen bonds defined for protein. 1716 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: 4.37 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4400 1.34 - 1.46: 2405 1.46 - 1.57: 8223 1.57 - 1.69: 20 1.69 - 1.81: 76 Bond restraints: 15124 Sorted by residual: bond pdb=" N GLU B 503 " pdb=" CA GLU B 503 " ideal model delta sigma weight residual 1.457 1.486 -0.029 6.40e-03 2.44e+04 2.06e+01 bond pdb=" N GLU A 503 " pdb=" CA GLU A 503 " ideal model delta sigma weight residual 1.457 1.486 -0.029 6.40e-03 2.44e+04 2.06e+01 bond pdb=" N GLU C 503 " pdb=" CA GLU C 503 " ideal model delta sigma weight residual 1.457 1.486 -0.029 6.40e-03 2.44e+04 2.06e+01 bond pdb=" N GLU D 503 " pdb=" CA GLU D 503 " ideal model delta sigma weight residual 1.457 1.485 -0.028 6.40e-03 2.44e+04 1.94e+01 bond pdb=" N VAL A 497 " pdb=" CA VAL A 497 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.75e+00 ... (remaining 15119 not shown) Histogram of bond angle deviations from ideal: 99.73 - 107.77: 523 107.77 - 115.81: 9122 115.81 - 123.85: 10321 123.85 - 131.88: 362 131.88 - 139.92: 16 Bond angle restraints: 20344 Sorted by residual: angle pdb=" C LYS A 116 " pdb=" N GLU A 117 " pdb=" CA GLU A 117 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C LYS D 116 " pdb=" N GLU D 117 " pdb=" CA GLU D 117 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C LYS B 116 " pdb=" N GLU B 117 " pdb=" CA GLU B 117 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C LYS C 116 " pdb=" N GLU C 117 " pdb=" CA GLU C 117 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.38e+01 angle pdb=" N ASP B 22 " pdb=" CA ASP B 22 " pdb=" C ASP B 22 " ideal model delta sigma weight residual 108.45 102.61 5.84 1.26e+00 6.30e-01 2.15e+01 ... (remaining 20339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 8132 17.18 - 34.36: 900 34.36 - 51.55: 200 51.55 - 68.73: 36 68.73 - 85.91: 20 Dihedral angle restraints: 9288 sinusoidal: 3992 harmonic: 5296 Sorted by residual: dihedral pdb=" CA ASP B 76 " pdb=" C ASP B 76 " pdb=" N LEU B 77 " pdb=" CA LEU B 77 " ideal model delta harmonic sigma weight residual -180.00 -153.37 -26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASP C 76 " pdb=" C ASP C 76 " pdb=" N LEU C 77 " pdb=" CA LEU C 77 " ideal model delta harmonic sigma weight residual 180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA ASP D 76 " pdb=" C ASP D 76 " pdb=" N LEU D 77 " pdb=" CA LEU D 77 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 9285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1641 0.057 - 0.114: 416 0.114 - 0.171: 168 0.171 - 0.228: 23 0.228 - 0.285: 8 Chirality restraints: 2256 Sorted by residual: chirality pdb=" CB ILE C 6 " pdb=" CA ILE C 6 " pdb=" CG1 ILE C 6 " pdb=" CG2 ILE C 6 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE D 6 " pdb=" CA ILE D 6 " pdb=" CG1 ILE D 6 " pdb=" CG2 ILE D 6 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE B 6 " pdb=" CA ILE B 6 " pdb=" CG1 ILE B 6 " pdb=" CG2 ILE B 6 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2253 not shown) Planarity restraints: 2564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 9 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.47e+00 pdb=" C LYS B 9 " 0.037 2.00e-02 2.50e+03 pdb=" O LYS B 9 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN B 10 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 9 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C LYS C 9 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS C 9 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN C 10 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 9 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C LYS A 9 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A 9 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 10 " 0.012 2.00e-02 2.50e+03 ... (remaining 2561 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 4842 2.87 - 3.38: 12020 3.38 - 3.89: 24467 3.89 - 4.39: 27338 4.39 - 4.90: 47837 Nonbonded interactions: 116504 Sorted by model distance: nonbonded pdb=" OG SER D 4 " pdb=" OD2 ASP D 76 " model vdw 2.368 3.040 nonbonded pdb=" OG SER B 4 " pdb=" OD2 ASP B 76 " model vdw 2.369 3.040 nonbonded pdb=" OG SER C 4 " pdb=" OD2 ASP C 76 " model vdw 2.369 3.040 nonbonded pdb=" OG SER A 4 " pdb=" OD2 ASP A 76 " model vdw 2.370 3.040 nonbonded pdb=" OG1 THR A 339 " pdb=" O LYS A 341 " model vdw 2.378 3.040 ... (remaining 116499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.920 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:10.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 0.006 0.056 15124 Z= 0.389 Angle : 1.057 12.055 20344 Z= 0.595 Chirality : 0.061 0.285 2256 Planarity : 0.006 0.045 2564 Dihedral : 15.320 85.911 5872 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.16), residues: 1788 helix: -3.71 (0.09), residues: 732 sheet: 0.05 (0.27), residues: 392 loop : -1.83 (0.20), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.006 TRP D 126 HIS 0.006 0.002 HIS A 415 PHE 0.031 0.002 PHE A 315 TYR 0.022 0.002 TYR A 326 ARG 0.016 0.001 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.762 Fit side-chains REVERT: A 141 ASN cc_start: 0.6872 (m-40) cc_final: 0.6356 (m-40) REVERT: A 422 ASP cc_start: 0.7603 (m-30) cc_final: 0.7394 (t0) REVERT: A 474 LYS cc_start: 0.7773 (mttt) cc_final: 0.7516 (mttt) REVERT: B 141 ASN cc_start: 0.6822 (m-40) cc_final: 0.6322 (m-40) REVERT: B 422 ASP cc_start: 0.7606 (m-30) cc_final: 0.7400 (t0) REVERT: D 141 ASN cc_start: 0.6873 (m-40) cc_final: 0.6357 (m-40) REVERT: D 422 ASP cc_start: 0.7605 (m-30) cc_final: 0.7395 (t0) REVERT: D 474 LYS cc_start: 0.7753 (mttt) cc_final: 0.7523 (mttt) REVERT: C 141 ASN cc_start: 0.6874 (m-40) cc_final: 0.6357 (m-40) REVERT: C 422 ASP cc_start: 0.7604 (m-30) cc_final: 0.7387 (t0) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 1.3731 time to fit residues: 405.6945 Evaluate side-chains 167 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.0060 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 141 optimal weight: 0.0870 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.3372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15124 Z= 0.159 Angle : 0.574 8.467 20344 Z= 0.312 Chirality : 0.045 0.170 2256 Planarity : 0.003 0.022 2564 Dihedral : 8.599 50.416 2076 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.27 % Allowed : 8.39 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.18), residues: 1788 helix: -1.18 (0.16), residues: 700 sheet: 0.09 (0.28), residues: 408 loop : -1.32 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 126 HIS 0.004 0.001 HIS D 415 PHE 0.009 0.001 PHE A 316 TYR 0.013 0.001 TYR C 314 ARG 0.005 0.000 ARG D 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 1.744 Fit side-chains REVERT: A 141 ASN cc_start: 0.6820 (m-40) cc_final: 0.6426 (m-40) REVERT: A 474 LYS cc_start: 0.7764 (mttt) cc_final: 0.7490 (mtmt) REVERT: B 141 ASN cc_start: 0.6817 (m-40) cc_final: 0.6432 (m-40) REVERT: D 141 ASN cc_start: 0.6824 (m-40) cc_final: 0.6432 (m-40) REVERT: D 474 LYS cc_start: 0.7769 (mttt) cc_final: 0.7497 (mtmt) REVERT: C 141 ASN cc_start: 0.6820 (m-40) cc_final: 0.6424 (m-40) outliers start: 21 outliers final: 5 residues processed: 187 average time/residue: 1.2728 time to fit residues: 262.4822 Evaluate side-chains 165 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 136 optimal weight: 0.0270 chunk 111 optimal weight: 0.0370 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 162 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 131 optimal weight: 0.0870 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS B 415 HIS D 415 HIS C 415 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15124 Z= 0.133 Angle : 0.526 9.810 20344 Z= 0.279 Chirality : 0.044 0.150 2256 Planarity : 0.002 0.019 2564 Dihedral : 7.665 49.940 2076 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.97 % Allowed : 10.57 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.19), residues: 1788 helix: -0.06 (0.18), residues: 700 sheet: 0.12 (0.27), residues: 408 loop : -1.14 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 126 HIS 0.005 0.001 HIS A 415 PHE 0.009 0.001 PHE C 315 TYR 0.012 0.001 TYR C 314 ARG 0.004 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.669 Fit side-chains REVERT: A 139 ARG cc_start: 0.6477 (mmm160) cc_final: 0.6063 (mmm160) REVERT: A 141 ASN cc_start: 0.6779 (m-40) cc_final: 0.6381 (m-40) REVERT: A 474 LYS cc_start: 0.7721 (mttt) cc_final: 0.7332 (mttt) REVERT: A 573 VAL cc_start: 0.5326 (t) cc_final: 0.5054 (m) REVERT: B 139 ARG cc_start: 0.6462 (mmm160) cc_final: 0.6048 (mmm160) REVERT: B 141 ASN cc_start: 0.6732 (m-40) cc_final: 0.6351 (m-40) REVERT: B 478 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7385 (ttpp) REVERT: D 139 ARG cc_start: 0.6479 (mmm160) cc_final: 0.6063 (mmm160) REVERT: D 141 ASN cc_start: 0.6787 (m-40) cc_final: 0.6399 (m-40) REVERT: D 474 LYS cc_start: 0.7722 (mttt) cc_final: 0.7385 (mttt) REVERT: C 139 ARG cc_start: 0.6500 (mmm160) cc_final: 0.6083 (mmm160) REVERT: C 141 ASN cc_start: 0.6769 (m-40) cc_final: 0.6373 (m-40) REVERT: C 478 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7374 (ttpp) REVERT: C 573 VAL cc_start: 0.5330 (t) cc_final: 0.5057 (m) outliers start: 16 outliers final: 6 residues processed: 198 average time/residue: 1.2708 time to fit residues: 277.2425 Evaluate side-chains 164 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 478 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 551 ASN C 551 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15124 Z= 0.353 Angle : 0.707 9.469 20344 Z= 0.372 Chirality : 0.049 0.168 2256 Planarity : 0.005 0.070 2564 Dihedral : 7.845 51.981 2076 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.02 % Allowed : 12.68 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 1788 helix: 0.35 (0.20), residues: 688 sheet: 0.02 (0.27), residues: 404 loop : -1.26 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP B 126 HIS 0.004 0.001 HIS C 415 PHE 0.017 0.002 PHE D 371 TYR 0.026 0.002 TYR C 314 ARG 0.010 0.001 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 175 time to evaluate : 1.835 Fit side-chains REVERT: A 141 ASN cc_start: 0.7200 (m-40) cc_final: 0.6968 (m-40) REVERT: A 474 LYS cc_start: 0.7710 (mttt) cc_final: 0.7285 (mttt) REVERT: B 141 ASN cc_start: 0.7189 (m-40) cc_final: 0.6954 (m-40) REVERT: D 141 ASN cc_start: 0.7208 (m-40) cc_final: 0.6984 (m-40) REVERT: D 474 LYS cc_start: 0.7691 (mttt) cc_final: 0.7437 (mttt) REVERT: C 59 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7491 (p0) REVERT: C 141 ASN cc_start: 0.7214 (m-40) cc_final: 0.6986 (m-40) outliers start: 50 outliers final: 16 residues processed: 208 average time/residue: 1.5197 time to fit residues: 343.9079 Evaluate side-chains 173 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 476 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN B 455 ASN D 455 ASN C 414 ASN C 455 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15124 Z= 0.201 Angle : 0.601 10.239 20344 Z= 0.316 Chirality : 0.045 0.152 2256 Planarity : 0.003 0.046 2564 Dihedral : 7.522 53.774 2076 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.08 % Allowed : 14.73 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1788 helix: 0.85 (0.20), residues: 680 sheet: 0.06 (0.27), residues: 396 loop : -1.24 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 126 HIS 0.003 0.001 HIS C 415 PHE 0.012 0.001 PHE C 315 TYR 0.017 0.001 TYR C 314 ARG 0.006 0.001 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 165 time to evaluate : 1.898 Fit side-chains REVERT: A 141 ASN cc_start: 0.7196 (m-40) cc_final: 0.6954 (m-40) REVERT: A 474 LYS cc_start: 0.7644 (mttt) cc_final: 0.7359 (mttt) REVERT: B 141 ASN cc_start: 0.7183 (m-40) cc_final: 0.6928 (m-40) REVERT: D 141 ASN cc_start: 0.7204 (m-40) cc_final: 0.6974 (m-40) REVERT: D 474 LYS cc_start: 0.7638 (mttt) cc_final: 0.7349 (mttt) REVERT: C 141 ASN cc_start: 0.7206 (m-40) cc_final: 0.6976 (m-40) outliers start: 51 outliers final: 17 residues processed: 201 average time/residue: 1.3767 time to fit residues: 302.9533 Evaluate side-chains 170 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 523 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 34 optimal weight: 0.0670 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 455 ASN B 414 ASN B 455 ASN D 414 ASN D 455 ASN C 455 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15124 Z= 0.177 Angle : 0.582 10.175 20344 Z= 0.304 Chirality : 0.045 0.150 2256 Planarity : 0.003 0.042 2564 Dihedral : 7.347 54.902 2076 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.05 % Allowed : 16.30 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1788 helix: 1.10 (0.20), residues: 692 sheet: 0.02 (0.27), residues: 396 loop : -1.09 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 126 HIS 0.003 0.001 HIS C 415 PHE 0.012 0.001 PHE C 315 TYR 0.015 0.001 TYR C 314 ARG 0.005 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 1.692 Fit side-chains REVERT: A 141 ASN cc_start: 0.7137 (m-40) cc_final: 0.6890 (m-40) REVERT: A 474 LYS cc_start: 0.7526 (mttt) cc_final: 0.7204 (mttt) REVERT: B 141 ASN cc_start: 0.7131 (m-40) cc_final: 0.6901 (m-40) REVERT: D 141 ASN cc_start: 0.7142 (m-40) cc_final: 0.6913 (m-40) REVERT: D 474 LYS cc_start: 0.7514 (mttt) cc_final: 0.7194 (mttt) REVERT: C 141 ASN cc_start: 0.7149 (m-40) cc_final: 0.6919 (m-40) REVERT: C 285 TYR cc_start: 0.7780 (m-80) cc_final: 0.7399 (m-80) REVERT: C 373 GLU cc_start: 0.5872 (OUTLIER) cc_final: 0.5667 (mm-30) outliers start: 34 outliers final: 12 residues processed: 207 average time/residue: 1.3079 time to fit residues: 298.2961 Evaluate side-chains 172 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 523 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 0.0870 chunk 98 optimal weight: 0.3980 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15124 Z= 0.163 Angle : 0.569 10.447 20344 Z= 0.296 Chirality : 0.044 0.150 2256 Planarity : 0.003 0.039 2564 Dihedral : 7.208 55.845 2076 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.84 % Allowed : 16.36 % Favored : 80.80 % 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: 0.19 (0.20), residues: 1788 helix: 1.36 (0.20), residues: 692 sheet: 0.02 (0.27), residues: 396 loop : -1.02 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 126 HIS 0.003 0.001 HIS C 415 PHE 0.012 0.001 PHE C 315 TYR 0.014 0.001 TYR C 314 ARG 0.004 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 171 time to evaluate : 1.787 Fit side-chains REVERT: A 141 ASN cc_start: 0.7083 (m-40) cc_final: 0.6800 (m-40) REVERT: A 285 TYR cc_start: 0.7886 (m-80) cc_final: 0.7476 (m-80) REVERT: A 474 LYS cc_start: 0.7516 (mttt) cc_final: 0.7213 (mttt) REVERT: B 141 ASN cc_start: 0.7077 (m-40) cc_final: 0.6807 (m-40) REVERT: B 285 TYR cc_start: 0.7886 (m-80) cc_final: 0.7478 (m-80) REVERT: D 141 ASN cc_start: 0.7067 (m-40) cc_final: 0.6818 (m-40) REVERT: D 285 TYR cc_start: 0.7888 (m-80) cc_final: 0.7475 (m-80) REVERT: D 474 LYS cc_start: 0.7497 (mttt) cc_final: 0.7205 (mttt) REVERT: C 141 ASN cc_start: 0.7068 (m-40) cc_final: 0.6815 (m-40) REVERT: C 285 TYR cc_start: 0.7785 (m-80) cc_final: 0.7457 (m-80) outliers start: 47 outliers final: 17 residues processed: 208 average time/residue: 1.2804 time to fit residues: 294.1104 Evaluate side-chains 174 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 523 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15124 Z= 0.319 Angle : 0.708 10.518 20344 Z= 0.367 Chirality : 0.048 0.195 2256 Planarity : 0.004 0.069 2564 Dihedral : 7.570 58.592 2076 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.66 % Allowed : 17.27 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1788 helix: 1.09 (0.20), residues: 680 sheet: -0.22 (0.27), residues: 396 loop : -1.06 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 126 HIS 0.004 0.001 HIS A 415 PHE 0.015 0.002 PHE B 315 TYR 0.023 0.002 TYR C 314 ARG 0.008 0.001 ARG D 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 155 time to evaluate : 1.735 Fit side-chains REVERT: A 152 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7908 (mp) REVERT: B 152 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7909 (mp) REVERT: D 152 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7913 (mp) REVERT: C 334 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8087 (mt) outliers start: 44 outliers final: 16 residues processed: 188 average time/residue: 1.3223 time to fit residues: 273.0089 Evaluate side-chains 166 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 523 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 0.2980 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 0.2980 chunk 152 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15124 Z= 0.189 Angle : 0.617 11.413 20344 Z= 0.319 Chirality : 0.046 0.148 2256 Planarity : 0.003 0.043 2564 Dihedral : 7.241 59.566 2076 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.23 % Allowed : 17.93 % Favored : 79.83 % 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: 0.16 (0.20), residues: 1788 helix: 1.41 (0.20), residues: 680 sheet: -0.18 (0.27), residues: 396 loop : -0.96 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 126 HIS 0.004 0.001 HIS B 415 PHE 0.012 0.001 PHE C 315 TYR 0.014 0.001 TYR C 314 ARG 0.008 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 163 time to evaluate : 2.082 Fit side-chains REVERT: A 285 TYR cc_start: 0.7944 (m-80) cc_final: 0.7484 (m-80) REVERT: B 285 TYR cc_start: 0.7944 (m-80) cc_final: 0.7488 (m-80) REVERT: D 285 TYR cc_start: 0.7946 (m-80) cc_final: 0.7487 (m-80) outliers start: 37 outliers final: 22 residues processed: 189 average time/residue: 1.2552 time to fit residues: 263.1153 Evaluate side-chains 178 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 523 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 0.0770 chunk 87 optimal weight: 0.1980 chunk 113 optimal weight: 1.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15124 Z= 0.191 Angle : 0.620 11.647 20344 Z= 0.320 Chirality : 0.045 0.146 2256 Planarity : 0.003 0.042 2564 Dihedral : 7.288 58.880 2076 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.33 % Allowed : 18.90 % Favored : 79.77 % 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: 0.27 (0.21), residues: 1788 helix: 1.52 (0.20), residues: 680 sheet: -0.15 (0.27), residues: 396 loop : -0.89 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 126 HIS 0.004 0.001 HIS D 415 PHE 0.012 0.001 PHE C 315 TYR 0.015 0.001 TYR C 314 ARG 0.008 0.000 ARG A 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.7953 (m-80) cc_final: 0.7510 (m-80) REVERT: B 110 GLU cc_start: 0.7259 (mp0) cc_final: 0.7016 (mp0) REVERT: B 285 TYR cc_start: 0.7954 (m-80) cc_final: 0.7511 (m-80) REVERT: D 110 GLU cc_start: 0.7249 (mp0) cc_final: 0.7003 (mp0) REVERT: D 285 TYR cc_start: 0.7952 (m-80) cc_final: 0.7507 (m-80) REVERT: D 464 GLU cc_start: 0.7440 (mp0) cc_final: 0.6817 (mp0) REVERT: C 110 GLU cc_start: 0.7248 (mp0) cc_final: 0.6999 (mp0) REVERT: C 285 TYR cc_start: 0.7902 (m-80) cc_final: 0.7440 (m-80) outliers start: 22 outliers final: 22 residues processed: 181 average time/residue: 1.3234 time to fit residues: 267.2221 Evaluate side-chains 193 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 523 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 146 optimal weight: 0.0670 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN B 330 ASN D 330 ASN C 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.227391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.196114 restraints weight = 16951.680| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.76 r_work: 0.4068 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15124 Z= 0.177 Angle : 0.605 11.673 20344 Z= 0.312 Chirality : 0.045 0.147 2256 Planarity : 0.003 0.043 2564 Dihedral : 7.194 58.419 2076 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.69 % Allowed : 18.48 % Favored : 79.83 % 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: 0.39 (0.21), residues: 1788 helix: 1.56 (0.21), residues: 692 sheet: -0.11 (0.27), residues: 396 loop : -0.79 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 126 HIS 0.003 0.001 HIS B 415 PHE 0.012 0.001 PHE C 315 TYR 0.013 0.001 TYR C 314 ARG 0.007 0.001 ARG D 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5572.75 seconds wall clock time: 103 minutes 8.33 seconds (6188.33 seconds total)