Starting phenix.real_space_refine on Fri Jun 28 13:59:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9emc_19817/06_2024/9emc_19817_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9emc_19817/06_2024/9emc_19817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9emc_19817/06_2024/9emc_19817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9emc_19817/06_2024/9emc_19817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9emc_19817/06_2024/9emc_19817_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9emc_19817/06_2024/9emc_19817_updated.pdb" } resolution = 3.26 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 75 5.16 5 C 9672 2.51 5 N 2718 2.21 5 O 3000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D GLU 377": "OE1" <-> "OE2" Residue "D GLU 378": "OE1" <-> "OE2" Residue "D GLU 445": "OE1" <-> "OE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "F GLU 300": "OE1" <-> "OE2" Residue "F GLU 376": "OE1" <-> "OE2" Residue "F GLU 377": "OE1" <-> "OE2" Residue "F GLU 378": "OE1" <-> "OE2" Residue "F GLU 445": "OE1" <-> "OE2" Residue "E GLU 300": "OE1" <-> "OE2" Residue "E GLU 376": "OE1" <-> "OE2" Residue "E GLU 377": "OE1" <-> "OE2" Residue "E GLU 378": "OE1" <-> "OE2" Residue "E GLU 445": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 15489 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2476 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 2 Chain: "D" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2623 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 9, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2476 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 2 Chain: "C" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2476 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 2 Chain: "F" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2623 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 9, 'TRANS': 327} Chain breaks: 1 Chain: "E" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2623 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 9, 'TRANS': 327} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.06, per 1000 atoms: 0.58 Number of scatterers: 15489 At special positions: 0 Unit cell: (129.043, 126.562, 87.6832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 75 16.00 P 18 15.00 Mg 6 11.99 O 3000 8.00 N 2718 7.00 C 9672 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=0, symmetry=0 Time building additional restraints: 6.19 Conformation dependent library (CDL) restraints added in 2.8 seconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 12 sheets defined 46.3% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 98 through 101 removed outlier: 4.159A pdb=" N VAL A 101 " --> pdb=" O GLY A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 101' Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.852A pdb=" N GLU A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.926A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 352 through 355 No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 368 through 381 Processing helix chain 'A' and resid 388 through 400 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 410 through 420 Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 115 through 126 removed outlier: 4.188A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 270 through 286 Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.730A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 348 through 353 removed outlier: 4.450A pdb=" N ARG D 353 " --> pdb=" O ASP D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 377 Processing helix chain 'D' and resid 384 through 396 Processing helix chain 'D' and resid 399 through 415 removed outlier: 3.896A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 432 Processing helix chain 'D' and resid 436 through 448 removed outlier: 3.936A pdb=" N GLU D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR D 446 " --> pdb=" O TYR D 442 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP D 448 " --> pdb=" O LYS D 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 58 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 98 through 101 removed outlier: 4.159A pdb=" N VAL B 101 " --> pdb=" O GLY B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 101' Processing helix chain 'B' and resid 108 through 118 Processing helix chain 'B' and resid 240 through 247 Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.852A pdb=" N GLU B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 309 through 319 removed outlier: 3.926A pdb=" N ARG B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 352 through 355 No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'B' and resid 388 through 400 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 410 through 420 Processing helix chain 'B' and resid 427 through 436 Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'C' and resid 43 through 58 Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 98 through 101 removed outlier: 4.159A pdb=" N VAL C 101 " --> pdb=" O GLY C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 101' Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 240 through 247 Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.853A pdb=" N GLU C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 309 through 319 removed outlier: 3.926A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 352 through 355 No H-bonds generated for 'chain 'C' and resid 352 through 355' Processing helix chain 'C' and resid 368 through 381 Processing helix chain 'C' and resid 388 through 400 Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 410 through 420 Processing helix chain 'C' and resid 427 through 436 Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'F' and resid 50 through 65 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 115 through 126 removed outlier: 4.189A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 306 through 315 removed outlier: 3.730A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 345 No H-bonds generated for 'chain 'F' and resid 343 through 345' Processing helix chain 'F' and resid 348 through 353 removed outlier: 4.450A pdb=" N ARG F 353 " --> pdb=" O ASP F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 377 Processing helix chain 'F' and resid 384 through 396 Processing helix chain 'F' and resid 399 through 415 removed outlier: 3.898A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 436 through 448 removed outlier: 3.936A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR F 446 " --> pdb=" O TYR F 442 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP F 448 " --> pdb=" O LYS F 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 65 Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 115 through 126 removed outlier: 4.188A pdb=" N SER E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 301 through 303 No H-bonds generated for 'chain 'E' and resid 301 through 303' Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.730A pdb=" N ARG E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'E' and resid 348 through 353 removed outlier: 4.450A pdb=" N ARG E 353 " --> pdb=" O ASP E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 377 Processing helix chain 'E' and resid 384 through 396 Processing helix chain 'E' and resid 399 through 415 removed outlier: 3.898A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 432 Processing helix chain 'E' and resid 436 through 448 removed outlier: 3.936A pdb=" N GLU E 445 " --> pdb=" O GLN E 441 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR E 446 " --> pdb=" O TYR E 442 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASP E 448 " --> pdb=" O LYS E 444 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 358 through 363 removed outlier: 7.113A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR A 363 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA A 69 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 327 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU A 68 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE A 329 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N GLY A 70 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 331 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 330 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 292 through 296 Processing sheet with id= C, first strand: chain 'D' and resid 355 through 359 removed outlier: 6.424A pdb=" N LEU D 324 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE D 75 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET D 326 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLY D 77 " --> pdb=" O MET D 326 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR D 328 " --> pdb=" O GLY D 77 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 289 through 293 Processing sheet with id= E, first strand: chain 'B' and resid 358 through 363 removed outlier: 7.112A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR B 363 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA B 69 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 327 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU B 68 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE B 329 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N GLY B 70 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER B 331 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 330 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 292 through 296 Processing sheet with id= G, first strand: chain 'C' and resid 358 through 363 removed outlier: 7.112A pdb=" N ALA C 65 " --> pdb=" O MET C 359 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE C 361 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU C 67 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR C 363 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA C 69 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL C 327 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU C 68 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE C 329 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N GLY C 70 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER C 331 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 330 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 292 through 296 Processing sheet with id= I, first strand: chain 'F' and resid 355 through 359 removed outlier: 6.425A pdb=" N LEU F 324 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE F 75 " --> pdb=" O LEU F 324 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET F 326 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY F 77 " --> pdb=" O MET F 326 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR F 328 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 289 through 293 Processing sheet with id= K, first strand: chain 'E' and resid 355 through 359 removed outlier: 6.424A pdb=" N LEU E 324 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE E 75 " --> pdb=" O LEU E 324 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET E 326 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLY E 77 " --> pdb=" O MET E 326 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR E 328 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 289 through 293 648 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4362 1.33 - 1.45: 2348 1.45 - 1.57: 8818 1.57 - 1.69: 18 1.69 - 1.81: 132 Bond restraints: 15678 Sorted by residual: bond pdb=" N ILE B 52 " pdb=" CA ILE B 52 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" N ILE C 52 " pdb=" CA ILE C 52 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.21e-02 6.83e+03 1.11e+01 bond pdb=" N ILE A 52 " pdb=" CA ILE A 52 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" N VAL A 327 " pdb=" CA VAL A 327 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 1.03e+01 bond pdb=" N VAL B 327 " pdb=" CA VAL B 327 " ideal model delta sigma weight residual 1.459 1.496 -0.038 1.20e-02 6.94e+03 9.86e+00 ... (remaining 15673 not shown) Histogram of bond angle deviations from ideal: 98.60 - 106.80: 540 106.80 - 115.00: 9445 115.00 - 123.20: 9991 123.20 - 131.40: 1152 131.40 - 139.61: 31 Bond angle restraints: 21159 Sorted by residual: angle pdb=" CA GLY C 297 " pdb=" C GLY C 297 " pdb=" O GLY C 297 " ideal model delta sigma weight residual 121.78 117.41 4.37 9.10e-01 1.21e+00 2.30e+01 angle pdb=" CA GLY A 297 " pdb=" C GLY A 297 " pdb=" O GLY A 297 " ideal model delta sigma weight residual 121.78 117.44 4.34 9.10e-01 1.21e+00 2.27e+01 angle pdb=" CA GLY B 297 " pdb=" C GLY B 297 " pdb=" O GLY B 297 " ideal model delta sigma weight residual 121.78 117.46 4.32 9.10e-01 1.21e+00 2.26e+01 angle pdb=" N ILE B 323 " pdb=" CA ILE B 323 " pdb=" C ILE B 323 " ideal model delta sigma weight residual 113.43 108.40 5.03 1.09e+00 8.42e-01 2.13e+01 angle pdb=" N ILE A 323 " pdb=" CA ILE A 323 " pdb=" C ILE A 323 " ideal model delta sigma weight residual 113.43 108.45 4.98 1.09e+00 8.42e-01 2.08e+01 ... (remaining 21154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8268 17.93 - 35.87: 1121 35.87 - 53.80: 286 53.80 - 71.73: 90 71.73 - 89.67: 30 Dihedral angle restraints: 9795 sinusoidal: 4125 harmonic: 5670 Sorted by residual: dihedral pdb=" CA ASP C 343 " pdb=" C ASP C 343 " pdb=" N ILE C 344 " pdb=" CA ILE C 344 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ASP B 343 " pdb=" C ASP B 343 " pdb=" N ILE B 344 " pdb=" CA ILE B 344 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP A 343 " pdb=" C ASP A 343 " pdb=" N ILE A 344 " pdb=" CA ILE A 344 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 9792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1796 0.082 - 0.163: 570 0.163 - 0.245: 102 0.245 - 0.326: 13 0.326 - 0.408: 6 Chirality restraints: 2487 Sorted by residual: chirality pdb=" CB VAL A 238 " pdb=" CA VAL A 238 " pdb=" CG1 VAL A 238 " pdb=" CG2 VAL A 238 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB VAL B 238 " pdb=" CA VAL B 238 " pdb=" CG1 VAL B 238 " pdb=" CG2 VAL B 238 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CB VAL C 238 " pdb=" CA VAL C 238 " pdb=" CG1 VAL C 238 " pdb=" CG2 VAL C 238 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 2484 not shown) Planarity restraints: 2679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 72 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C PRO B 72 " 0.073 2.00e-02 2.50e+03 pdb=" O PRO B 72 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY B 73 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 72 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C PRO A 72 " -0.072 2.00e-02 2.50e+03 pdb=" O PRO A 72 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY A 73 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 72 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C PRO C 72 " 0.072 2.00e-02 2.50e+03 pdb=" O PRO C 72 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY C 73 " -0.024 2.00e-02 2.50e+03 ... (remaining 2676 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 232 2.64 - 3.20: 12736 3.20 - 3.77: 24860 3.77 - 4.33: 35806 4.33 - 4.90: 56830 Nonbonded interactions: 130464 Sorted by model distance: nonbonded pdb=" O3G ATP A 501 " pdb="MG MG A 502 " model vdw 2.075 2.170 nonbonded pdb=" O3G ATP C 501 " pdb="MG MG C 502 " model vdw 2.076 2.170 nonbonded pdb=" O3G ATP B 501 " pdb="MG MG B 502 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR F 84 " pdb="MG MG F 502 " model vdw 2.088 2.170 nonbonded pdb=" OG1 THR D 84 " pdb="MG MG D 502 " model vdw 2.089 2.170 ... (remaining 130459 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.390 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: 5.960 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 42.410 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 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:2.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 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 : 0.011 0.111 15678 Z= 0.695 Angle : 1.344 9.972 21159 Z= 0.825 Chirality : 0.082 0.408 2487 Planarity : 0.009 0.058 2679 Dihedral : 18.595 89.668 6129 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.44 % Allowed : 18.65 % Favored : 79.90 % 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: -3.73 (0.16), residues: 1947 helix: -3.87 (0.09), residues: 993 sheet: -1.79 (0.31), residues: 252 loop : 0.02 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.005 TRP D 283 HIS 0.011 0.003 HIS B 241 PHE 0.018 0.004 PHE B 312 TYR 0.044 0.003 TYR A 314 ARG 0.023 0.002 ARG F 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 487 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 3 residues processed: 502 average time/residue: 0.2725 time to fit residues: 196.4169 Evaluate side-chains 264 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 261 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain F residue 380 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 420 ASN D 302 HIS D 341 GLN B 42 GLN B 115 ASN ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN C 13 GLN C 115 ASN C 332 ASN C 335 ASN C 373 GLN ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN E 25 HIS E 341 GLN E 404 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15678 Z= 0.205 Angle : 0.578 8.615 21159 Z= 0.305 Chirality : 0.042 0.233 2487 Planarity : 0.004 0.035 2679 Dihedral : 10.162 82.278 2339 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.49 % Allowed : 23.83 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 1947 helix: -1.26 (0.14), residues: 1020 sheet: -1.40 (0.29), residues: 288 loop : 0.52 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 283 HIS 0.007 0.001 HIS A 316 PHE 0.023 0.002 PHE F 297 TYR 0.012 0.001 TYR E 430 ARG 0.007 0.001 ARG D 414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 256 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 313 ASN cc_start: 0.5721 (m110) cc_final: 0.5507 (m110) outliers start: 58 outliers final: 29 residues processed: 305 average time/residue: 0.2350 time to fit residues: 110.0905 Evaluate side-chains 245 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 42 GLN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 GLN B 332 ASN C 335 ASN F 27 HIS E 275 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.7735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15678 Z= 0.272 Angle : 0.600 9.451 21159 Z= 0.317 Chirality : 0.043 0.280 2487 Planarity : 0.004 0.054 2679 Dihedral : 9.246 83.728 2336 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.61 % Allowed : 23.89 % Favored : 72.50 % 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 (0.18), residues: 1947 helix: 0.03 (0.16), residues: 1029 sheet: -0.89 (0.29), residues: 288 loop : 0.21 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 283 HIS 0.022 0.002 HIS F 302 PHE 0.034 0.002 PHE D 257 TYR 0.017 0.001 TYR E 430 ARG 0.011 0.001 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 168 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 244 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8479 (mt) outliers start: 60 outliers final: 27 residues processed: 222 average time/residue: 0.2514 time to fit residues: 83.6672 Evaluate side-chains 169 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN F 240 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.8969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15678 Z= 0.411 Angle : 0.592 7.871 21159 Z= 0.311 Chirality : 0.044 0.204 2487 Planarity : 0.004 0.039 2679 Dihedral : 9.234 89.934 2336 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.67 % Allowed : 23.29 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 1947 helix: 0.59 (0.16), residues: 1035 sheet: -0.55 (0.31), residues: 276 loop : 0.32 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 283 HIS 0.009 0.001 HIS F 302 PHE 0.025 0.002 PHE F 297 TYR 0.017 0.001 TYR D 430 ARG 0.008 0.001 ARG D 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 131 time to evaluate : 1.717 Fit side-chains revert: symmetry clash REVERT: A 116 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8375 (t80) REVERT: F 405 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8512 (mp) REVERT: F 428 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7615 (tpm170) outliers start: 61 outliers final: 33 residues processed: 186 average time/residue: 0.2562 time to fit residues: 71.6880 Evaluate side-chains 151 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 42 GLN C 42 GLN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.9307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15678 Z= 0.304 Angle : 0.509 8.643 21159 Z= 0.268 Chirality : 0.042 0.183 2487 Planarity : 0.003 0.032 2679 Dihedral : 8.905 89.335 2336 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.89 % Allowed : 23.53 % Favored : 73.59 % 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: 1947 helix: 1.05 (0.17), residues: 1032 sheet: -0.36 (0.31), residues: 285 loop : 0.13 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 283 HIS 0.004 0.001 HIS F 302 PHE 0.017 0.002 PHE F 297 TYR 0.013 0.001 TYR D 446 ARG 0.006 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 121 time to evaluate : 1.767 Fit side-chains revert: symmetry clash REVERT: C 454 TYR cc_start: 0.8751 (m-80) cc_final: 0.8497 (m-80) REVERT: F 405 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8453 (mp) REVERT: F 428 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7603 (tpm170) outliers start: 48 outliers final: 26 residues processed: 161 average time/residue: 0.2777 time to fit residues: 68.8566 Evaluate side-chains 142 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.8379 moved from start: 0.9537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15678 Z= 0.289 Angle : 0.511 7.910 21159 Z= 0.266 Chirality : 0.042 0.211 2487 Planarity : 0.003 0.029 2679 Dihedral : 8.679 85.006 2336 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.07 % Allowed : 23.35 % Favored : 73.59 % 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: 0.96 (0.19), residues: 1947 helix: 1.27 (0.17), residues: 1038 sheet: -0.24 (0.32), residues: 270 loop : 0.19 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 283 HIS 0.003 0.001 HIS F 302 PHE 0.016 0.001 PHE F 297 TYR 0.009 0.001 TYR A 314 ARG 0.007 0.000 ARG F 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 122 time to evaluate : 1.763 Fit side-chains revert: symmetry clash REVERT: C 326 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8775 (mp) REVERT: C 454 TYR cc_start: 0.8786 (m-80) cc_final: 0.8473 (m-80) REVERT: F 135 THR cc_start: 0.6675 (p) cc_final: 0.6268 (p) REVERT: F 405 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8444 (mp) REVERT: F 428 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7562 (tpm170) outliers start: 51 outliers final: 34 residues processed: 166 average time/residue: 0.2652 time to fit residues: 69.3494 Evaluate side-chains 150 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 113 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 187 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN F 341 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.9610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15678 Z= 0.150 Angle : 0.455 7.971 21159 Z= 0.236 Chirality : 0.040 0.200 2487 Planarity : 0.003 0.026 2679 Dihedral : 8.180 71.813 2336 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.47 % Allowed : 24.01 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 1947 helix: 1.50 (0.17), residues: 1035 sheet: 0.00 (0.33), residues: 255 loop : 0.25 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 283 HIS 0.003 0.001 HIS C 18 PHE 0.013 0.001 PHE F 297 TYR 0.007 0.001 TYR F 430 ARG 0.006 0.000 ARG F 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 125 time to evaluate : 1.809 Fit side-chains REVERT: A 116 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8272 (t80) REVERT: C 326 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8732 (mp) REVERT: C 454 TYR cc_start: 0.8798 (m-80) cc_final: 0.8490 (m-80) REVERT: F 135 THR cc_start: 0.6731 (p) cc_final: 0.6301 (p) REVERT: F 341 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7459 (mt0) REVERT: F 405 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8354 (mp) REVERT: F 428 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7553 (tpm170) outliers start: 41 outliers final: 24 residues processed: 161 average time/residue: 0.2475 time to fit residues: 61.1874 Evaluate side-chains 146 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 341 GLN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 255 GLN B 408 GLN ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.9714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15678 Z= 0.304 Angle : 0.519 11.794 21159 Z= 0.268 Chirality : 0.042 0.269 2487 Planarity : 0.003 0.030 2679 Dihedral : 8.110 78.577 2336 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.53 % Allowed : 24.13 % Favored : 73.35 % 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: 1.30 (0.20), residues: 1947 helix: 1.53 (0.17), residues: 1038 sheet: 0.09 (0.33), residues: 255 loop : 0.27 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 283 HIS 0.003 0.001 HIS B 241 PHE 0.023 0.002 PHE E 257 TYR 0.018 0.001 TYR D 446 ARG 0.008 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 114 time to evaluate : 1.894 Fit side-chains REVERT: D 428 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7470 (tpm170) REVERT: C 326 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8748 (mp) REVERT: C 454 TYR cc_start: 0.8816 (m-80) cc_final: 0.8465 (m-80) REVERT: F 135 THR cc_start: 0.6952 (p) cc_final: 0.6567 (p) REVERT: F 405 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8469 (mp) REVERT: F 428 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7548 (tpm170) outliers start: 42 outliers final: 30 residues processed: 152 average time/residue: 0.2420 time to fit residues: 57.4887 Evaluate side-chains 146 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.9798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15678 Z= 0.214 Angle : 0.481 9.391 21159 Z= 0.248 Chirality : 0.041 0.204 2487 Planarity : 0.003 0.035 2679 Dihedral : 8.012 76.965 2336 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.53 % Allowed : 24.13 % Favored : 73.35 % 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: 1.40 (0.20), residues: 1947 helix: 1.63 (0.17), residues: 1035 sheet: 0.12 (0.33), residues: 255 loop : 0.28 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 283 HIS 0.004 0.001 HIS C 305 PHE 0.013 0.001 PHE F 297 TYR 0.015 0.001 TYR A 102 ARG 0.007 0.000 ARG F 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 118 time to evaluate : 1.823 Fit side-chains REVERT: D 428 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7482 (tpm170) REVERT: C 326 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8728 (mp) REVERT: C 454 TYR cc_start: 0.8835 (m-80) cc_final: 0.8502 (m-80) REVERT: F 135 THR cc_start: 0.6795 (p) cc_final: 0.6446 (p) REVERT: F 405 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8411 (mp) REVERT: F 428 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7552 (tpm170) outliers start: 42 outliers final: 33 residues processed: 156 average time/residue: 0.2458 time to fit residues: 59.7652 Evaluate side-chains 147 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 110 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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: 0.8338 moved from start: 0.9841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15678 Z= 0.183 Angle : 0.476 10.735 21159 Z= 0.246 Chirality : 0.041 0.246 2487 Planarity : 0.003 0.031 2679 Dihedral : 7.870 76.478 2336 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.35 % Allowed : 24.25 % Favored : 73.41 % 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: 1.48 (0.20), residues: 1947 helix: 1.70 (0.17), residues: 1035 sheet: 0.20 (0.33), residues: 255 loop : 0.30 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 283 HIS 0.006 0.001 HIS E 302 PHE 0.025 0.001 PHE D 257 TYR 0.018 0.001 TYR D 446 ARG 0.007 0.000 ARG F 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 117 time to evaluate : 1.790 Fit side-chains REVERT: D 428 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7501 (tpm170) REVERT: C 326 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8717 (mp) REVERT: C 454 TYR cc_start: 0.8830 (m-80) cc_final: 0.8505 (m-80) REVERT: F 135 THR cc_start: 0.6781 (p) cc_final: 0.6431 (p) REVERT: F 405 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8398 (mp) REVERT: F 428 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7547 (tpm170) outliers start: 39 outliers final: 31 residues processed: 153 average time/residue: 0.2492 time to fit residues: 59.2458 Evaluate side-chains 151 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 19 optimal weight: 0.2980 chunk 28 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.062716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.049962 restraints weight = 43675.307| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.59 r_work: 0.2565 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.9888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15678 Z= 0.197 Angle : 0.475 9.464 21159 Z= 0.245 Chirality : 0.041 0.265 2487 Planarity : 0.003 0.045 2679 Dihedral : 7.818 76.923 2336 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.41 % Allowed : 24.07 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.20), residues: 1947 helix: 1.71 (0.17), residues: 1035 sheet: 0.23 (0.33), residues: 255 loop : 0.34 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 283 HIS 0.006 0.001 HIS E 302 PHE 0.013 0.001 PHE F 297 TYR 0.018 0.001 TYR A 102 ARG 0.007 0.000 ARG B 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.25 seconds wall clock time: 52 minutes 36.64 seconds (3156.64 seconds total)