Starting phenix.real_space_refine on Sun Jul 21 15:23:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/07_2024/8wy4_37915.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/07_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_37915/07_2024/8wy4_37915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/07_2024/8wy4_37915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/07_2024/8wy4_37915.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/07_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-5388/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: 9.48, per 1000 atoms: 0.64 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: 5.52 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: 1.76 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: 6.16 Time building geometry restraints manager: 6.13 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 2.440 nonbonded pdb=" OG SER B 4 " pdb=" OD2 ASP B 76 " model vdw 2.369 2.440 nonbonded pdb=" OG SER C 4 " pdb=" OD2 ASP C 76 " model vdw 2.369 2.440 nonbonded pdb=" OG SER A 4 " pdb=" OD2 ASP A 76 " model vdw 2.370 2.440 nonbonded pdb=" OG1 THR A 339 " pdb=" O LYS A 341 " model vdw 2.378 2.440 ... (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 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: 2.450 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 45.100 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.440 ------------------------------------------------------------------------------- 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 : 1.697 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: 1.2683 time to fit residues: 375.7485 Evaluate side-chains 167 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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: 0.9980 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 ASN ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15124 Z= 0.216 Angle : 0.620 8.853 20344 Z= 0.332 Chirality : 0.046 0.167 2256 Planarity : 0.004 0.031 2564 Dihedral : 8.422 51.340 2076 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.48 % Allowed : 8.33 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.18), residues: 1788 helix: -1.15 (0.17), residues: 692 sheet: 0.03 (0.27), residues: 404 loop : -1.29 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 126 HIS 0.004 0.001 HIS A 415 PHE 0.012 0.002 PHE B 371 TYR 0.017 0.001 TYR C 314 ARG 0.008 0.001 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 220 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 179 time to evaluate : 1.792 Fit side-chains REVERT: A 1 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6603 (tmt) REVERT: A 285 TYR cc_start: 0.7831 (m-80) cc_final: 0.7541 (m-80) REVERT: B 59 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7286 (p0) REVERT: B 285 TYR cc_start: 0.7818 (m-80) cc_final: 0.7521 (m-80) REVERT: D 1 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6600 (tmt) REVERT: D 285 TYR cc_start: 0.7830 (m-80) cc_final: 0.7539 (m-80) REVERT: D 422 ASP cc_start: 0.7672 (m-30) cc_final: 0.7471 (t0) REVERT: C 285 TYR cc_start: 0.7746 (m-80) cc_final: 0.7488 (m-80) REVERT: C 422 ASP cc_start: 0.7663 (m-30) cc_final: 0.7462 (t0) outliers start: 41 outliers final: 20 residues processed: 195 average time/residue: 1.2553 time to fit residues: 269.3643 Evaluate side-chains 181 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 549 VAL 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: 0.9990 chunk 136 optimal weight: 0.6980 chunk 111 optimal weight: 0.0570 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS A 544 ASN B 415 HIS B 544 ASN D 415 HIS D 544 ASN C 415 HIS C 544 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15124 Z= 0.165 Angle : 0.556 9.888 20344 Z= 0.296 Chirality : 0.044 0.152 2256 Planarity : 0.003 0.029 2564 Dihedral : 7.416 50.745 2076 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.11 % Allowed : 11.71 % Favored : 86.17 % 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: -0.68 (0.19), residues: 1788 helix: 0.04 (0.19), residues: 700 sheet: 0.11 (0.28), residues: 404 loop : -1.20 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 126 HIS 0.004 0.001 HIS A 415 PHE 0.010 0.001 PHE C 315 TYR 0.015 0.001 TYR C 314 ARG 0.006 0.001 ARG B 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 210 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 1.655 Fit side-chains REVERT: A 139 ARG cc_start: 0.6610 (mmm160) cc_final: 0.6215 (mmm160) REVERT: A 285 TYR cc_start: 0.7806 (m-80) cc_final: 0.7486 (m-80) REVERT: A 392 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6973 (p0) REVERT: A 478 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7420 (ttpp) REVERT: B 139 ARG cc_start: 0.6605 (mmm160) cc_final: 0.6218 (mmm160) REVERT: B 285 TYR cc_start: 0.7804 (m-80) cc_final: 0.7487 (m-80) REVERT: B 478 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7446 (ttpp) REVERT: D 139 ARG cc_start: 0.6611 (mmm160) cc_final: 0.6214 (mmm160) REVERT: D 285 TYR cc_start: 0.7804 (m-80) cc_final: 0.7482 (m-80) REVERT: D 478 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7413 (ttpp) REVERT: C 139 ARG cc_start: 0.6611 (mmm160) cc_final: 0.6214 (mmm160) REVERT: C 285 TYR cc_start: 0.7745 (m-80) cc_final: 0.7458 (m-80) REVERT: C 392 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7096 (p0) REVERT: C 478 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7445 (ttpp) outliers start: 35 outliers final: 16 residues processed: 194 average time/residue: 1.3666 time to fit residues: 290.3633 Evaluate side-chains 178 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 550 ASN A 551 ASN B 544 ASN B 550 ASN B 551 ASN D 550 ASN D 551 ASN C 544 ASN C 550 ASN C 551 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15124 Z= 0.412 Angle : 0.766 10.203 20344 Z= 0.401 Chirality : 0.050 0.171 2256 Planarity : 0.005 0.082 2564 Dihedral : 7.882 52.000 2076 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.74 % Allowed : 14.19 % Favored : 82.07 % 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: -0.77 (0.19), residues: 1788 helix: 0.24 (0.19), residues: 688 sheet: -0.19 (0.26), residues: 396 loop : -1.38 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 126 HIS 0.003 0.001 HIS A 63 PHE 0.018 0.003 PHE A 371 TYR 0.027 0.002 TYR C 314 ARG 0.011 0.001 ARG D 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 236 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 174 time to evaluate : 1.669 Fit side-chains REVERT: A 59 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7680 (p0) REVERT: A 285 TYR cc_start: 0.7987 (m-80) cc_final: 0.7561 (m-80) REVERT: B 59 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7680 (p0) REVERT: B 285 TYR cc_start: 0.7989 (m-80) cc_final: 0.7564 (m-80) REVERT: D 110 GLU cc_start: 0.7205 (mp0) cc_final: 0.6925 (mp0) REVERT: D 285 TYR cc_start: 0.7988 (m-80) cc_final: 0.7560 (m-80) REVERT: C 59 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7685 (p0) outliers start: 62 outliers final: 15 residues processed: 219 average time/residue: 1.2658 time to fit residues: 304.9392 Evaluate side-chains 189 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 0.0470 chunk 43 optimal weight: 4.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 455 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2841 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= 0.221 Angle : 0.618 10.086 20344 Z= 0.326 Chirality : 0.046 0.154 2256 Planarity : 0.004 0.052 2564 Dihedral : 7.383 53.880 2076 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.02 % Allowed : 16.73 % Favored : 80.25 % 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: -0.37 (0.20), residues: 1788 helix: 0.84 (0.20), residues: 680 sheet: -0.20 (0.27), residues: 396 loop : -1.28 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 126 HIS 0.004 0.001 HIS C 415 PHE 0.012 0.001 PHE C 315 TYR 0.016 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: 50 poor density : 166 time to evaluate : 1.729 Fit side-chains REVERT: A 285 TYR cc_start: 0.7961 (m-80) cc_final: 0.7507 (m-80) REVERT: A 392 ASP cc_start: 0.7582 (p0) cc_final: 0.7336 (p0) REVERT: A 545 MET cc_start: 0.8467 (tpt) cc_final: 0.8233 (tpt) REVERT: B 285 TYR cc_start: 0.7967 (m-80) cc_final: 0.7511 (m-80) REVERT: B 478 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7583 (ttpp) REVERT: D 285 TYR cc_start: 0.7964 (m-80) cc_final: 0.7509 (m-80) REVERT: C 392 ASP cc_start: 0.7567 (p0) cc_final: 0.7330 (p0) REVERT: C 478 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7590 (ttpp) outliers start: 50 outliers final: 15 residues processed: 206 average time/residue: 1.2468 time to fit residues: 283.4386 Evaluate side-chains 178 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 476 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 144 optimal weight: 0.0370 chunk 80 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN B 414 ASN D 414 ASN C 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15124 Z= 0.166 Angle : 0.573 10.576 20344 Z= 0.300 Chirality : 0.045 0.150 2256 Planarity : 0.003 0.042 2564 Dihedral : 6.905 54.778 2076 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.84 % Allowed : 16.91 % Favored : 80.25 % 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: 0.05 (0.20), residues: 1788 helix: 1.31 (0.20), residues: 680 sheet: -0.13 (0.27), residues: 396 loop : -1.09 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 126 HIS 0.003 0.001 HIS C 415 PHE 0.012 0.001 PHE C 315 TYR 0.013 0.001 TYR C 314 ARG 0.003 0.000 ARG D 332 *********************** 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 214 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 167 time to evaluate : 1.653 Fit side-chains REVERT: A 285 TYR cc_start: 0.7951 (m-80) cc_final: 0.7536 (m-80) REVERT: A 392 ASP cc_start: 0.7518 (p0) cc_final: 0.7300 (p0) REVERT: B 285 TYR cc_start: 0.7952 (m-80) cc_final: 0.7540 (m-80) REVERT: D 285 TYR cc_start: 0.7953 (m-80) cc_final: 0.7536 (m-80) REVERT: C 392 ASP cc_start: 0.7513 (p0) cc_final: 0.7301 (p0) outliers start: 47 outliers final: 20 residues processed: 197 average time/residue: 1.1611 time to fit residues: 253.8249 Evaluate side-chains 176 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 426 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 549 VAL 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: 0.8980 chunk 99 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 0.0370 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- 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: 0.7667 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15124 Z= 0.259 Angle : 0.644 10.734 20344 Z= 0.335 Chirality : 0.046 0.155 2256 Planarity : 0.004 0.061 2564 Dihedral : 7.150 56.882 2076 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.54 % Allowed : 18.06 % Favored : 79.41 % 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: 0.03 (0.20), residues: 1788 helix: 1.28 (0.20), residues: 680 sheet: -0.22 (0.27), residues: 396 loop : -1.03 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 126 HIS 0.004 0.001 HIS B 415 PHE 0.014 0.002 PHE C 315 TYR 0.020 0.002 TYR C 314 ARG 0.007 0.001 ARG C 481 *********************** 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 195 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 1.826 Fit side-chains revert: symmetry clash REVERT: A 152 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7906 (mp) REVERT: A 285 TYR cc_start: 0.7971 (m-80) cc_final: 0.7558 (m-80) REVERT: A 334 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8086 (mt) REVERT: A 392 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7347 (p0) REVERT: B 110 GLU cc_start: 0.7357 (mp0) cc_final: 0.7070 (mp0) REVERT: B 152 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7903 (mp) REVERT: B 285 TYR cc_start: 0.7974 (m-80) cc_final: 0.7562 (m-80) REVERT: B 334 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8033 (mt) REVERT: D 152 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7908 (mp) REVERT: D 285 TYR cc_start: 0.7972 (m-80) cc_final: 0.7559 (m-80) REVERT: D 334 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8088 (mt) REVERT: C 152 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7881 (mp) REVERT: C 334 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8025 (mt) REVERT: C 392 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7345 (p0) outliers start: 42 outliers final: 16 residues processed: 179 average time/residue: 1.2076 time to fit residues: 240.0228 Evaluate side-chains 177 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 549 VAL 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: 1.9990 chunk 103 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15124 Z= 0.216 Angle : 0.623 11.229 20344 Z= 0.323 Chirality : 0.046 0.151 2256 Planarity : 0.004 0.057 2564 Dihedral : 6.930 58.770 2076 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.02 % Allowed : 18.60 % Favored : 78.38 % 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: 0.14 (0.20), residues: 1788 helix: 1.40 (0.20), residues: 680 sheet: -0.21 (0.27), residues: 396 loop : -0.97 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 126 HIS 0.004 0.001 HIS D 415 PHE 0.013 0.001 PHE A 315 TYR 0.016 0.001 TYR C 314 ARG 0.007 0.001 ARG A 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 206 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 156 time to evaluate : 1.793 Fit side-chains revert: symmetry clash REVERT: A 285 TYR cc_start: 0.7958 (m-80) cc_final: 0.7538 (m-80) REVERT: A 334 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8091 (mt) REVERT: A 392 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7342 (p0) REVERT: B 110 GLU cc_start: 0.7360 (mp0) cc_final: 0.7078 (mp0) REVERT: B 285 TYR cc_start: 0.7962 (m-80) cc_final: 0.7541 (m-80) REVERT: B 334 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8100 (mt) REVERT: D 285 TYR cc_start: 0.7961 (m-80) cc_final: 0.7538 (m-80) REVERT: D 334 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8099 (mt) REVERT: C 334 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8091 (mt) REVERT: C 392 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7351 (p0) outliers start: 50 outliers final: 22 residues processed: 190 average time/residue: 1.1153 time to fit residues: 236.4544 Evaluate side-chains 184 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 334 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 392 ASP 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 549 VAL 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: 8.9990 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 146 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15124 Z= 0.209 Angle : 0.620 11.507 20344 Z= 0.320 Chirality : 0.045 0.150 2256 Planarity : 0.003 0.055 2564 Dihedral : 7.037 59.922 2076 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.90 % Allowed : 19.50 % Favored : 77.60 % 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: 1.50 (0.20), residues: 680 sheet: -0.25 (0.27), residues: 396 loop : -0.96 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 126 HIS 0.004 0.001 HIS D 415 PHE 0.013 0.001 PHE C 315 TYR 0.016 0.001 TYR C 314 ARG 0.007 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 208 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 160 time to evaluate : 1.793 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.6716 (mmm160) cc_final: 0.6095 (mmm160) REVERT: A 285 TYR cc_start: 0.7963 (m-80) cc_final: 0.7571 (m-80) REVERT: A 317 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8607 (tp) REVERT: A 334 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8096 (mt) REVERT: A 392 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7342 (p0) REVERT: B 110 GLU cc_start: 0.7394 (mp0) cc_final: 0.7122 (mp0) REVERT: B 285 TYR cc_start: 0.7969 (m-80) cc_final: 0.7584 (m-80) REVERT: B 317 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8604 (tp) REVERT: B 334 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8094 (mt) REVERT: D 285 TYR cc_start: 0.7969 (m-80) cc_final: 0.7581 (m-80) REVERT: D 317 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8599 (tp) REVERT: D 334 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8066 (mt) REVERT: C 139 ARG cc_start: 0.6738 (mmm160) cc_final: 0.6117 (mmm160) REVERT: C 334 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8115 (mt) REVERT: C 392 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7336 (p0) outliers start: 48 outliers final: 20 residues processed: 192 average time/residue: 1.2892 time to fit residues: 273.9776 Evaluate side-chains 187 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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 317 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7648 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15124 Z= 0.221 Angle : 0.638 11.665 20344 Z= 0.328 Chirality : 0.045 0.151 2256 Planarity : 0.004 0.058 2564 Dihedral : 7.077 58.954 2076 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.17 % Allowed : 20.35 % Favored : 77.48 % 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: 0.22 (0.21), residues: 1788 helix: 1.52 (0.20), residues: 680 sheet: -0.23 (0.27), residues: 396 loop : -0.93 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 126 HIS 0.004 0.001 HIS D 415 PHE 0.013 0.001 PHE C 315 TYR 0.016 0.001 TYR C 314 ARG 0.007 0.001 ARG D 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 204 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.6699 (mmm160) cc_final: 0.6083 (mmm160) REVERT: A 285 TYR cc_start: 0.7965 (m-80) cc_final: 0.7547 (m-80) REVERT: A 317 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8614 (tp) REVERT: A 334 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8074 (mt) REVERT: A 392 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7285 (p0) REVERT: B 110 GLU cc_start: 0.7423 (mp0) cc_final: 0.7066 (mp0) REVERT: B 139 ARG cc_start: 0.6729 (mmm160) cc_final: 0.6090 (mmm160) REVERT: B 285 TYR cc_start: 0.7970 (m-80) cc_final: 0.7553 (m-80) REVERT: B 317 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8610 (tp) REVERT: B 334 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8063 (mt) REVERT: D 139 ARG cc_start: 0.6722 (mmm160) cc_final: 0.6128 (mmm160) REVERT: D 285 TYR cc_start: 0.7970 (m-80) cc_final: 0.7550 (m-80) REVERT: D 317 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8607 (tp) REVERT: D 334 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8062 (mt) REVERT: C 139 ARG cc_start: 0.6722 (mmm160) cc_final: 0.6090 (mmm160) REVERT: C 334 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8095 (mt) REVERT: C 392 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7284 (p0) outliers start: 36 outliers final: 22 residues processed: 189 average time/residue: 1.2474 time to fit residues: 263.6770 Evaluate side-chains 195 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 317 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 143 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 125 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 550 ASN B 330 ASN D 330 ASN D 550 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.225517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.194022 restraints weight = 16998.257| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.77 r_work: 0.4046 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15124 Z= 0.176 Angle : 0.602 11.654 20344 Z= 0.309 Chirality : 0.045 0.148 2256 Planarity : 0.003 0.044 2564 Dihedral : 6.963 59.139 2076 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.36 % Allowed : 20.23 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.35 (0.21), residues: 1788 helix: 1.66 (0.21), residues: 680 sheet: -0.20 (0.27), residues: 396 loop : -0.87 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 126 HIS 0.003 0.001 HIS D 415 PHE 0.013 0.001 PHE C 315 TYR 0.013 0.001 TYR C 314 ARG 0.007 0.001 ARG A 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5263.27 seconds wall clock time: 93 minutes 6.94 seconds (5586.94 seconds total)