Starting phenix.real_space_refine on Fri Mar 15 21:57:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7v_0364/03_2024/6n7v_0364_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7v_0364/03_2024/6n7v_0364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7v_0364/03_2024/6n7v_0364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7v_0364/03_2024/6n7v_0364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7v_0364/03_2024/6n7v_0364_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7v_0364/03_2024/6n7v_0364_updated.pdb" } resolution = 3.8 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= 0.005 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 31 5.49 5 Mg 5 5.21 5 S 78 5.16 5 C 7963 2.51 5 N 2258 2.21 5 O 2526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 363": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12861 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2093 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2111 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 4, 'TRANS': 269} Chain breaks: 3 Chain: "C" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2127 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 4, 'TRANS': 271} Chain breaks: 3 Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2086 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2003 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1971 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 320 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.17, per 1000 atoms: 0.56 Number of scatterers: 12861 At special positions: 0 Unit cell: (77.4, 125.56, 135.88, 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 78 16.00 P 31 15.00 Mg 5 11.99 O 2526 8.00 N 2258 7.00 C 7963 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: 4.98 Conformation dependent library (CDL) restraints added in 2.3 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2862 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 6 sheets defined 30.9% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.574A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.665A pdb=" N ILE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 386 removed outlier: 3.971A pdb=" N GLU A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 removed outlier: 3.705A pdb=" N ALA A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.915A pdb=" N ARG B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 331 Processing helix chain 'B' and resid 346 through 357 Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 377 through 386 removed outlier: 3.830A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 414 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 438 through 453 Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.503A pdb=" N LYS C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 removed outlier: 3.585A pdb=" N GLN C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 351 through 357 removed outlier: 3.543A pdb=" N GLY C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 374 removed outlier: 3.655A pdb=" N ARG C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 removed outlier: 3.664A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.779A pdb=" N VAL C 430 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 431 " --> pdb=" O ILE C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 456 Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'D' and resid 269 through 276 removed outlier: 4.151A pdb=" N ARG D 272 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU D 273 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG D 274 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE D 275 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 331 removed outlier: 3.501A pdb=" N GLN D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 357 Processing helix chain 'D' and resid 366 through 369 No H-bonds generated for 'chain 'D' and resid 366 through 369' Processing helix chain 'D' and resid 371 through 374 No H-bonds generated for 'chain 'D' and resid 371 through 374' Processing helix chain 'D' and resid 377 through 386 removed outlier: 4.104A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 416 Processing helix chain 'D' and resid 440 through 455 removed outlier: 3.684A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing helix chain 'D' and resid 491 through 494 No H-bonds generated for 'chain 'D' and resid 491 through 494' Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 318 through 328 Processing helix chain 'E' and resid 348 through 357 removed outlier: 3.756A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 371 removed outlier: 3.762A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 386 removed outlier: 3.837A pdb=" N GLU E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 414 Processing helix chain 'E' and resid 440 through 456 removed outlier: 3.921A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 477 No H-bonds generated for 'chain 'E' and resid 475 through 477' Processing helix chain 'E' and resid 491 through 493 No H-bonds generated for 'chain 'E' and resid 491 through 493' Processing helix chain 'F' and resid 318 through 328 Processing helix chain 'F' and resid 348 through 357 Processing helix chain 'F' and resid 366 through 371 removed outlier: 4.093A pdb=" N ARG F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 386 removed outlier: 3.583A pdb=" N GLU F 384 " --> pdb=" O GLN F 380 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU F 385 " --> pdb=" O TRP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 414 Processing helix chain 'F' and resid 440 through 456 Processing helix chain 'F' and resid 475 through 477 No H-bonds generated for 'chain 'F' and resid 475 through 477' Processing helix chain 'F' and resid 491 through 493 No H-bonds generated for 'chain 'F' and resid 491 through 493' Processing sheet with id= A, first strand: chain 'A' and resid 542 through 544 removed outlier: 7.253A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 542 through 544 removed outlier: 7.069A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 498 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 463 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 542 through 544 removed outlier: 6.763A pdb=" N VAL C 516 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR C 532 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C 514 " --> pdb=" O TYR C 532 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU C 460 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N VAL C 310 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL C 462 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 528 through 533 removed outlier: 7.099A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR D 498 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU D 460 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N VAL D 310 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL D 462 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 528 through 534 removed outlier: 6.900A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR E 498 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU E 502 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU E 460 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL E 310 " --> pdb=" O LEU E 460 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL E 462 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N SER E 312 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N CYS E 464 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 528 through 534 removed outlier: 6.809A pdb=" N VAL F 516 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR F 532 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL F 514 " --> pdb=" O TYR F 532 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE F 499 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR F 498 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU F 502 " --> pdb=" O THR F 311 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU F 460 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL F 310 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL F 462 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N SER F 312 " --> pdb=" O VAL F 462 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N CYS F 464 " --> pdb=" O SER F 312 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LYS F 336 " --> pdb=" O ASP F 419 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE F 421 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY F 338 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU F 423 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA F 340 " --> pdb=" O LEU F 423 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1077 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: 3.10 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2149 1.31 - 1.44: 3211 1.44 - 1.57: 7489 1.57 - 1.69: 56 1.69 - 1.82: 132 Bond restraints: 13037 Sorted by residual: bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C6 TTP F 700 " pdb=" N1 TTP F 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.423 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C6 TTP C 700 " pdb=" N1 TTP C 700 " ideal model delta sigma weight residual 1.337 1.422 -0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 13032 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.64: 307 106.64 - 113.47: 7279 113.47 - 120.29: 4839 120.29 - 127.11: 5051 127.11 - 133.94: 112 Bond angle restraints: 17588 Sorted by residual: angle pdb=" PA TTP E 700 " pdb=" O3A TTP E 700 " pdb=" PB TTP E 700 " ideal model delta sigma weight residual 120.50 132.76 -12.26 3.00e+00 1.11e-01 1.67e+01 angle pdb=" PB TTP E 700 " pdb=" O3B TTP E 700 " pdb=" PG TTP E 700 " ideal model delta sigma weight residual 120.50 132.75 -12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" PA TTP F 700 " pdb=" O3A TTP F 700 " pdb=" PB TTP F 700 " ideal model delta sigma weight residual 120.50 132.68 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" PB TTP F 700 " pdb=" O3B TTP F 700 " pdb=" PG TTP F 700 " ideal model delta sigma weight residual 120.50 132.68 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" PB TTP B 700 " pdb=" O3B TTP B 700 " pdb=" PG TTP B 700 " ideal model delta sigma weight residual 120.50 132.65 -12.15 3.00e+00 1.11e-01 1.64e+01 ... (remaining 17583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 7641 35.22 - 70.45: 118 70.45 - 105.67: 12 105.67 - 140.89: 6 140.89 - 176.12: 8 Dihedral angle restraints: 7785 sinusoidal: 3315 harmonic: 4470 Sorted by residual: dihedral pdb=" O2G TTP E 700 " pdb=" O3B TTP E 700 " pdb=" PG TTP E 700 " pdb=" PB TTP E 700 " ideal model delta sinusoidal sigma weight residual -180.00 -3.88 -176.12 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C2 TTP C 700 " pdb=" C1' TTP C 700 " pdb=" N1 TTP C 700 " pdb=" O4' TTP C 700 " ideal model delta sinusoidal sigma weight residual -58.32 114.54 -172.85 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C2 TTP E 700 " pdb=" C1' TTP E 700 " pdb=" N1 TTP E 700 " pdb=" O4' TTP E 700 " ideal model delta sinusoidal sigma weight residual 301.68 134.33 167.36 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 7782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1462 0.051 - 0.103: 407 0.103 - 0.154: 120 0.154 - 0.205: 5 0.205 - 0.257: 9 Chirality restraints: 2003 Sorted by residual: chirality pdb=" C3' TTP D 700 " pdb=" C2' TTP D 700 " pdb=" C4' TTP D 700 " pdb=" O3' TTP D 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C3' TTP B 700 " pdb=" C2' TTP B 700 " pdb=" C4' TTP B 700 " pdb=" O3' TTP B 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C3' TTP E 700 " pdb=" C2' TTP E 700 " pdb=" C4' TTP E 700 " pdb=" O3' TTP E 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 2000 not shown) Planarity restraints: 2165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 412 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C MET E 412 " 0.031 2.00e-02 2.50e+03 pdb=" O MET E 412 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG E 413 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 510 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO D 511 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 511 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 511 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET F 412 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C MET F 412 " 0.031 2.00e-02 2.50e+03 pdb=" O MET F 412 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG F 413 " -0.010 2.00e-02 2.50e+03 ... (remaining 2162 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 194 2.68 - 3.23: 10977 3.23 - 3.79: 18927 3.79 - 4.34: 25861 4.34 - 4.90: 42599 Nonbonded interactions: 98558 Sorted by model distance: nonbonded pdb=" OE1 GLN E 343 " pdb="MG MG E 701 " model vdw 2.119 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.144 2.170 nonbonded pdb=" O2G TTP F 700 " pdb="MG MG F 701 " model vdw 2.145 2.170 nonbonded pdb=" OE1 GLN F 343 " pdb="MG MG F 701 " model vdw 2.198 2.170 nonbonded pdb=" O1B TTP C 700 " pdb="MG MG C 701 " model vdw 2.206 2.170 ... (remaining 98553 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' and (resid 264 through 277 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 or resid 439 or (resid 440 and (name N or name \ CA or name C or name O or name CB )) or resid 441 through 506 or resid 510 throu \ gh 545)) selection = (chain 'B' and (resid 264 through 277 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 or resid 439 or (resid 440 and (name N or name \ CA or name C or name O or name CB )) or resid 441 through 506 or resid 510 throu \ gh 545)) selection = (chain 'C' and (resid 264 through 277 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 or resid 439 or (resid 440 and (name N or name \ CA or name C or name O or name CB )) or resid 441 through 545)) selection = (chain 'D' and (resid 264 through 277 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 or resid 439 through 506 or resid 510 through 5 \ 45)) selection = (chain 'E' and (resid 264 through 277 or resid 285 through 506 or resid 510 thro \ ugh 545)) selection = (chain 'F' and (resid 264 through 506 or resid 510 through 545)) } 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 group one per residue 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.590 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 34.650 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 0.005 0.090 13037 Z= 0.292 Angle : 0.892 12.258 17588 Z= 0.471 Chirality : 0.053 0.257 2003 Planarity : 0.004 0.045 2165 Dihedral : 14.423 176.116 4923 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.15 % Allowed : 3.11 % Favored : 96.74 % 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: -3.41 (0.18), residues: 1554 helix: -2.69 (0.16), residues: 523 sheet: -0.74 (0.29), residues: 311 loop : -2.57 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 541 HIS 0.012 0.002 HIS C 425 PHE 0.017 0.002 PHE A 523 TYR 0.012 0.001 TYR B 535 ARG 0.006 0.001 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 380 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.7033 (mm110) cc_final: 0.6611 (tm-30) REVERT: A 329 TRP cc_start: 0.7059 (m-10) cc_final: 0.6551 (m-10) REVERT: A 341 MET cc_start: 0.5231 (mmt) cc_final: 0.5000 (mmm) REVERT: A 356 LEU cc_start: 0.8364 (tp) cc_final: 0.8096 (mt) REVERT: A 411 TYR cc_start: 0.6837 (t80) cc_final: 0.6374 (t80) REVERT: A 412 MET cc_start: 0.8601 (ttm) cc_final: 0.7745 (tmm) REVERT: A 418 CYS cc_start: 0.6168 (p) cc_final: 0.4839 (m) REVERT: A 419 ASP cc_start: 0.7546 (m-30) cc_final: 0.7268 (m-30) REVERT: A 448 LYS cc_start: 0.8818 (mttt) cc_final: 0.8536 (mttp) REVERT: A 506 GLN cc_start: 0.7896 (pt0) cc_final: 0.7692 (pt0) REVERT: A 510 MET cc_start: 0.6259 (mtp) cc_final: 0.5920 (mpp) REVERT: B 445 LEU cc_start: 0.8701 (tp) cc_final: 0.8458 (mm) REVERT: B 494 GLN cc_start: 0.8832 (mt0) cc_final: 0.8555 (mt0) REVERT: B 533 MET cc_start: 0.7255 (mtm) cc_final: 0.6911 (mtm) REVERT: C 316 MET cc_start: 0.7829 (mmm) cc_final: 0.7499 (mmt) REVERT: C 328 GLN cc_start: 0.8164 (mm110) cc_final: 0.7925 (mm-40) REVERT: C 408 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7205 (mmtt) REVERT: D 307 VAL cc_start: 0.7904 (t) cc_final: 0.7480 (t) REVERT: D 323 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7686 (mmp80) REVERT: D 341 MET cc_start: 0.8393 (mmp) cc_final: 0.8141 (mmt) REVERT: D 537 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7517 (mmtm) REVERT: E 278 HIS cc_start: 0.8299 (t70) cc_final: 0.7821 (t-90) REVERT: E 306 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6640 (mt-10) REVERT: F 298 LYS cc_start: 0.7403 (ttmm) cc_final: 0.7038 (mmtp) REVERT: F 476 GLU cc_start: 0.7268 (mp0) cc_final: 0.6864 (mp0) outliers start: 2 outliers final: 1 residues processed: 381 average time/residue: 0.2881 time to fit residues: 149.2476 Evaluate side-chains 191 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 504 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN C 324 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN D 278 HIS ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN D 475 HIS E 358 ASN ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 ASN F 343 GLN F 364 GLN F 392 HIS ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13037 Z= 0.303 Angle : 0.676 8.077 17588 Z= 0.333 Chirality : 0.045 0.155 2003 Planarity : 0.004 0.064 2165 Dihedral : 16.150 177.820 1942 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.97 % Allowed : 12.16 % Favored : 84.88 % 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: -2.25 (0.20), residues: 1554 helix: -0.94 (0.21), residues: 519 sheet: -0.64 (0.29), residues: 318 loop : -2.30 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 329 HIS 0.007 0.001 HIS B 357 PHE 0.024 0.002 PHE E 321 TYR 0.015 0.002 TYR F 535 ARG 0.006 0.001 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 210 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.8534 (tp) cc_final: 0.8298 (mt) REVERT: A 411 TYR cc_start: 0.6542 (t80) cc_final: 0.6092 (t80) REVERT: A 419 ASP cc_start: 0.7380 (m-30) cc_final: 0.7159 (m-30) REVERT: A 510 MET cc_start: 0.6236 (mtp) cc_final: 0.5931 (mpp) REVERT: B 341 MET cc_start: 0.8655 (mmt) cc_final: 0.8328 (tpp) REVERT: B 533 MET cc_start: 0.7686 (mtm) cc_final: 0.7458 (mtm) REVERT: C 333 MET cc_start: 0.8337 (mpp) cc_final: 0.8062 (mmp) REVERT: D 323 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7467 (mtm110) REVERT: D 352 ASP cc_start: 0.7259 (t0) cc_final: 0.6240 (t70) REVERT: D 385 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7631 (pp) REVERT: D 537 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8136 (mmtp) REVERT: E 306 GLU cc_start: 0.7821 (mt-10) cc_final: 0.6919 (mt-10) REVERT: E 514 VAL cc_start: 0.8961 (m) cc_final: 0.8672 (p) REVERT: E 533 MET cc_start: 0.8205 (mpp) cc_final: 0.7825 (mpp) REVERT: F 298 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7401 (mmtp) REVERT: F 359 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7267 (ttp80) REVERT: F 412 MET cc_start: 0.4955 (OUTLIER) cc_final: 0.4734 (ptp) REVERT: F 539 THR cc_start: 0.6354 (p) cc_final: 0.5892 (t) outliers start: 40 outliers final: 28 residues processed: 241 average time/residue: 0.2347 time to fit residues: 82.2645 Evaluate side-chains 207 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 412 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 156 optimal weight: 0.0770 chunk 128 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 ASN F 364 GLN ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13037 Z= 0.306 Angle : 0.656 8.065 17588 Z= 0.324 Chirality : 0.045 0.159 2003 Planarity : 0.004 0.065 2165 Dihedral : 15.952 171.096 1938 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.41 % Allowed : 13.42 % Favored : 83.17 % 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: -1.91 (0.21), residues: 1554 helix: -0.52 (0.22), residues: 542 sheet: -0.70 (0.30), residues: 319 loop : -2.13 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 541 HIS 0.007 0.001 HIS B 357 PHE 0.021 0.002 PHE E 321 TYR 0.020 0.002 TYR A 547 ARG 0.005 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 178 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.8670 (tp) cc_final: 0.8399 (mt) REVERT: A 380 GLN cc_start: 0.8543 (mp10) cc_final: 0.8150 (mp10) REVERT: A 411 TYR cc_start: 0.6853 (t80) cc_final: 0.6350 (t80) REVERT: A 510 MET cc_start: 0.6316 (mtp) cc_final: 0.6000 (mpp) REVERT: B 316 MET cc_start: 0.8065 (mmp) cc_final: 0.7337 (mmp) REVERT: B 533 MET cc_start: 0.7757 (mtm) cc_final: 0.7500 (mtm) REVERT: C 333 MET cc_start: 0.8396 (mpp) cc_final: 0.7959 (mmp) REVERT: D 323 ARG cc_start: 0.7800 (ttm110) cc_final: 0.7570 (mtm110) REVERT: D 352 ASP cc_start: 0.7086 (t0) cc_final: 0.6182 (t70) REVERT: D 385 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7606 (pp) REVERT: D 470 ASP cc_start: 0.9036 (p0) cc_final: 0.8761 (p0) REVERT: D 537 LYS cc_start: 0.8705 (mmmt) cc_final: 0.8228 (mmtp) REVERT: E 341 MET cc_start: 0.7926 (mmm) cc_final: 0.7720 (tpp) REVERT: F 298 LYS cc_start: 0.7813 (ttmm) cc_final: 0.7311 (mmtp) outliers start: 46 outliers final: 36 residues processed: 214 average time/residue: 0.2776 time to fit residues: 88.1917 Evaluate side-chains 201 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 357 HIS Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 443 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN D 325 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 444 ASN ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13037 Z= 0.180 Angle : 0.552 8.119 17588 Z= 0.271 Chirality : 0.042 0.163 2003 Planarity : 0.003 0.062 2165 Dihedral : 15.377 165.063 1938 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.74 % Allowed : 15.20 % Favored : 82.06 % 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: -1.37 (0.21), residues: 1554 helix: 0.13 (0.23), residues: 529 sheet: -0.46 (0.31), residues: 307 loop : -1.92 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 541 HIS 0.007 0.001 HIS E 278 PHE 0.017 0.001 PHE E 321 TYR 0.024 0.001 TYR A 547 ARG 0.004 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 169 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.8666 (tp) cc_final: 0.8407 (mt) REVERT: A 380 GLN cc_start: 0.8560 (mp10) cc_final: 0.8132 (mp10) REVERT: A 411 TYR cc_start: 0.7043 (t80) cc_final: 0.6616 (t80) REVERT: B 316 MET cc_start: 0.8100 (mmp) cc_final: 0.7352 (mmp) REVERT: B 341 MET cc_start: 0.8660 (mmt) cc_final: 0.8414 (tpp) REVERT: B 533 MET cc_start: 0.7698 (mtm) cc_final: 0.7482 (mtm) REVERT: C 333 MET cc_start: 0.8448 (mpp) cc_final: 0.8161 (mmp) REVERT: D 323 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7334 (mmp80) REVERT: D 470 ASP cc_start: 0.9029 (p0) cc_final: 0.8746 (p0) REVERT: D 537 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8204 (mmtp) REVERT: E 306 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6533 (mt-10) REVERT: E 441 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6613 (tmm) REVERT: F 298 LYS cc_start: 0.7778 (ttmm) cc_final: 0.7222 (mmtp) outliers start: 37 outliers final: 30 residues processed: 195 average time/residue: 0.2300 time to fit residues: 66.4357 Evaluate side-chains 193 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 441 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 114 optimal weight: 0.0470 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 HIS F 494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13037 Z= 0.143 Angle : 0.528 8.308 17588 Z= 0.257 Chirality : 0.042 0.162 2003 Planarity : 0.003 0.059 2165 Dihedral : 14.903 160.520 1938 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.82 % Allowed : 15.86 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.22), residues: 1554 helix: 0.42 (0.24), residues: 534 sheet: -0.33 (0.32), residues: 305 loop : -1.73 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 541 HIS 0.004 0.001 HIS B 425 PHE 0.014 0.001 PHE E 321 TYR 0.008 0.001 TYR F 535 ARG 0.003 0.000 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.8653 (tp) cc_final: 0.8406 (mt) REVERT: A 380 GLN cc_start: 0.8537 (mp10) cc_final: 0.8110 (mp10) REVERT: A 411 TYR cc_start: 0.7277 (t80) cc_final: 0.6743 (t80) REVERT: B 316 MET cc_start: 0.8134 (mmp) cc_final: 0.7380 (mmp) REVERT: B 542 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7717 (pp) REVERT: D 470 ASP cc_start: 0.9013 (p0) cc_final: 0.8727 (p0) REVERT: D 526 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.6823 (p0) REVERT: E 306 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6575 (mt-10) REVERT: E 441 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6256 (tmm) REVERT: E 495 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8905 (mp) REVERT: E 510 MET cc_start: 0.8364 (mmm) cc_final: 0.8110 (mmm) REVERT: F 298 LYS cc_start: 0.7414 (ttmm) cc_final: 0.7061 (mmtp) REVERT: F 341 MET cc_start: 0.5744 (mmt) cc_final: 0.5251 (tpt) outliers start: 38 outliers final: 24 residues processed: 196 average time/residue: 0.2231 time to fit residues: 64.7421 Evaluate side-chains 187 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 388 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.1980 chunk 30 optimal weight: 0.0020 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 0.0060 chunk 153 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 425 HIS B 465 HIS C 468 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 475 HIS ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13037 Z= 0.128 Angle : 0.515 7.722 17588 Z= 0.250 Chirality : 0.041 0.164 2003 Planarity : 0.002 0.060 2165 Dihedral : 14.542 161.993 1938 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.59 % Allowed : 16.46 % Favored : 80.95 % 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: -0.84 (0.22), residues: 1554 helix: 0.57 (0.24), residues: 542 sheet: -0.26 (0.32), residues: 308 loop : -1.59 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 541 HIS 0.006 0.001 HIS B 465 PHE 0.013 0.001 PHE E 321 TYR 0.007 0.001 TYR D 532 ARG 0.003 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.7202 (tp40) cc_final: 0.6697 (tp40) REVERT: A 356 LEU cc_start: 0.8782 (tp) cc_final: 0.8473 (mt) REVERT: A 380 GLN cc_start: 0.8533 (mp10) cc_final: 0.8099 (mp10) REVERT: A 411 TYR cc_start: 0.7134 (t80) cc_final: 0.6555 (t80) REVERT: A 510 MET cc_start: 0.6497 (mpp) cc_final: 0.5651 (mpp) REVERT: A 533 MET cc_start: 0.6942 (mtp) cc_final: 0.6717 (ttm) REVERT: B 316 MET cc_start: 0.8182 (mmp) cc_final: 0.7718 (mmp) REVERT: B 425 HIS cc_start: 0.4881 (OUTLIER) cc_final: 0.4628 (t-90) REVERT: D 470 ASP cc_start: 0.9100 (p0) cc_final: 0.8810 (p0) REVERT: E 306 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6420 (mt-10) REVERT: E 441 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6424 (tmm) REVERT: E 495 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8890 (mp) REVERT: E 510 MET cc_start: 0.8442 (mmm) cc_final: 0.8218 (mmm) REVERT: F 298 LYS cc_start: 0.7362 (ttmm) cc_final: 0.6990 (mmtp) REVERT: F 316 MET cc_start: 0.6667 (mmm) cc_final: 0.6154 (mtp) REVERT: F 341 MET cc_start: 0.5716 (mmt) cc_final: 0.5218 (tpt) outliers start: 35 outliers final: 26 residues processed: 200 average time/residue: 0.2107 time to fit residues: 63.8558 Evaluate side-chains 192 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 321 PHE Chi-restraints excluded: chain F residue 388 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 6.9990 chunk 87 optimal weight: 0.0870 chunk 112 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13037 Z= 0.286 Angle : 0.635 8.566 17588 Z= 0.311 Chirality : 0.045 0.161 2003 Planarity : 0.004 0.064 2165 Dihedral : 14.847 164.036 1938 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.11 % Allowed : 16.46 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1554 helix: 0.42 (0.23), residues: 539 sheet: -0.50 (0.31), residues: 317 loop : -1.60 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 541 HIS 0.008 0.001 HIS B 465 PHE 0.015 0.002 PHE E 321 TYR 0.019 0.002 TYR A 547 ARG 0.003 0.001 ARG E 504 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 161 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 328 GLN cc_start: 0.6916 (tp40) cc_final: 0.6581 (mm-40) REVERT: A 333 MET cc_start: 0.8640 (mtt) cc_final: 0.7897 (mpp) REVERT: A 356 LEU cc_start: 0.8749 (tp) cc_final: 0.8389 (mt) REVERT: A 380 GLN cc_start: 0.8526 (mp10) cc_final: 0.8087 (mp10) REVERT: A 411 TYR cc_start: 0.6961 (t80) cc_final: 0.6280 (t80) REVERT: A 438 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.6777 (pp20) REVERT: A 510 MET cc_start: 0.6645 (mpp) cc_final: 0.5841 (mpp) REVERT: B 316 MET cc_start: 0.8021 (mmp) cc_final: 0.7512 (mmp) REVERT: D 470 ASP cc_start: 0.9052 (p0) cc_final: 0.8844 (p0) REVERT: D 526 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7109 (p0) REVERT: E 441 MET cc_start: 0.6903 (tmm) cc_final: 0.6443 (tmm) REVERT: E 495 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8861 (mp) REVERT: E 510 MET cc_start: 0.8494 (mmm) cc_final: 0.8004 (mpp) REVERT: F 298 LYS cc_start: 0.7886 (ttmm) cc_final: 0.7419 (mmtp) REVERT: F 316 MET cc_start: 0.5774 (mmm) cc_final: 0.5516 (mtp) REVERT: F 341 MET cc_start: 0.5508 (mmt) cc_final: 0.5039 (tpt) outliers start: 42 outliers final: 34 residues processed: 191 average time/residue: 0.2241 time to fit residues: 63.8834 Evaluate side-chains 190 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 454 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.1980 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 0.0770 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 0.0980 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 overall best weight: 0.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 468 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13037 Z= 0.142 Angle : 0.546 8.519 17588 Z= 0.264 Chirality : 0.042 0.163 2003 Planarity : 0.003 0.064 2165 Dihedral : 14.483 169.697 1938 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.37 % Allowed : 17.49 % Favored : 80.13 % 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: -0.62 (0.22), residues: 1554 helix: 0.84 (0.24), residues: 529 sheet: -0.25 (0.32), residues: 305 loop : -1.45 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 541 HIS 0.006 0.001 HIS B 425 PHE 0.013 0.001 PHE E 321 TYR 0.006 0.001 TYR F 535 ARG 0.003 0.000 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: A 328 GLN cc_start: 0.6793 (tp40) cc_final: 0.6076 (tp40) REVERT: A 333 MET cc_start: 0.8447 (mtt) cc_final: 0.7890 (mpp) REVERT: A 356 LEU cc_start: 0.8759 (tp) cc_final: 0.8442 (mt) REVERT: A 380 GLN cc_start: 0.8558 (mp10) cc_final: 0.8135 (mp10) REVERT: A 411 TYR cc_start: 0.6890 (t80) cc_final: 0.6207 (t80) REVERT: A 510 MET cc_start: 0.6650 (mpp) cc_final: 0.5873 (mpp) REVERT: B 316 MET cc_start: 0.7907 (mmp) cc_final: 0.7419 (mmp) REVERT: D 470 ASP cc_start: 0.9065 (p0) cc_final: 0.8847 (p0) REVERT: E 306 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6525 (mt-10) REVERT: E 441 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6338 (tmm) REVERT: E 495 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8897 (mp) REVERT: F 298 LYS cc_start: 0.7369 (ttmm) cc_final: 0.7066 (mptt) REVERT: F 316 MET cc_start: 0.6697 (mmm) cc_final: 0.6338 (mtp) REVERT: F 341 MET cc_start: 0.5706 (mmt) cc_final: 0.5195 (tpt) outliers start: 32 outliers final: 27 residues processed: 186 average time/residue: 0.2369 time to fit residues: 65.9330 Evaluate side-chains 183 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 388 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 93 optimal weight: 0.3980 chunk 151 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS C 468 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13037 Z= 0.210 Angle : 0.585 9.576 17588 Z= 0.282 Chirality : 0.043 0.166 2003 Planarity : 0.003 0.068 2165 Dihedral : 14.503 177.820 1938 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.59 % Allowed : 17.64 % Favored : 79.76 % 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 (0.22), residues: 1554 helix: 0.71 (0.24), residues: 538 sheet: -0.30 (0.32), residues: 312 loop : -1.48 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 541 HIS 0.004 0.001 HIS B 425 PHE 0.014 0.001 PHE E 321 TYR 0.020 0.001 TYR A 547 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.8692 (tp) cc_final: 0.8448 (mt) REVERT: A 380 GLN cc_start: 0.8548 (mp10) cc_final: 0.8118 (mp10) REVERT: A 411 TYR cc_start: 0.6918 (t80) cc_final: 0.6211 (t80) REVERT: A 510 MET cc_start: 0.6632 (mpp) cc_final: 0.5899 (mpp) REVERT: B 316 MET cc_start: 0.7903 (mmp) cc_final: 0.7422 (mmp) REVERT: E 306 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6529 (mt-10) REVERT: E 441 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6415 (tmm) REVERT: E 495 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8873 (mp) REVERT: F 298 LYS cc_start: 0.7539 (ttmm) cc_final: 0.7323 (mmtm) REVERT: F 316 MET cc_start: 0.5821 (mmm) cc_final: 0.5562 (mtp) REVERT: F 341 MET cc_start: 0.5714 (mmt) cc_final: 0.5280 (tpt) outliers start: 35 outliers final: 29 residues processed: 179 average time/residue: 0.2230 time to fit residues: 59.6441 Evaluate side-chains 184 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 309 MET Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 388 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.0870 chunk 71 optimal weight: 0.8980 chunk 104 optimal weight: 0.0270 chunk 158 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 468 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13037 Z= 0.135 Angle : 0.553 9.550 17588 Z= 0.264 Chirality : 0.042 0.165 2003 Planarity : 0.003 0.067 2165 Dihedral : 14.106 170.325 1938 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.22 % Allowed : 18.24 % Favored : 79.54 % 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: -0.49 (0.22), residues: 1554 helix: 0.96 (0.24), residues: 529 sheet: -0.14 (0.32), residues: 301 loop : -1.39 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 541 HIS 0.003 0.001 HIS B 425 PHE 0.013 0.001 PHE E 321 TYR 0.006 0.001 TYR F 535 ARG 0.003 0.000 ARG C 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: A 333 MET cc_start: 0.8464 (mtt) cc_final: 0.7709 (mpp) REVERT: A 356 LEU cc_start: 0.8820 (tp) cc_final: 0.8525 (mt) REVERT: A 380 GLN cc_start: 0.8519 (mp10) cc_final: 0.8115 (mp10) REVERT: A 411 TYR cc_start: 0.6609 (t80) cc_final: 0.6159 (t80) REVERT: A 460 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8340 (tt) REVERT: A 510 MET cc_start: 0.6647 (mpp) cc_final: 0.5952 (mpp) REVERT: B 316 MET cc_start: 0.7852 (mmp) cc_final: 0.7352 (mmp) REVERT: E 306 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6480 (mt-10) REVERT: E 441 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.6656 (tmm) REVERT: E 495 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8855 (mp) REVERT: F 298 LYS cc_start: 0.7294 (ttmm) cc_final: 0.7018 (mptt) REVERT: F 316 MET cc_start: 0.6692 (mmm) cc_final: 0.6038 (mtp) REVERT: F 341 MET cc_start: 0.5670 (mmt) cc_final: 0.5166 (tpt) REVERT: F 510 MET cc_start: 0.6390 (tpp) cc_final: 0.6171 (ptm) outliers start: 30 outliers final: 24 residues processed: 183 average time/residue: 0.2193 time to fit residues: 60.3012 Evaluate side-chains 179 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 468 ASN Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 388 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 343 GLN C 468 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.118136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.098660 restraints weight = 31768.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.101160 restraints weight = 19146.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.102875 restraints weight = 13243.221| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13037 Z= 0.156 Angle : 0.559 9.569 17588 Z= 0.267 Chirality : 0.042 0.162 2003 Planarity : 0.003 0.067 2165 Dihedral : 14.094 175.504 1938 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.22 % Allowed : 18.46 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1554 helix: 0.88 (0.24), residues: 538 sheet: -0.17 (0.32), residues: 304 loop : -1.40 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 541 HIS 0.002 0.001 HIS C 465 PHE 0.013 0.001 PHE E 321 TYR 0.020 0.001 TYR A 547 ARG 0.002 0.000 ARG C 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2554.68 seconds wall clock time: 47 minutes 9.04 seconds (2829.04 seconds total)