Starting phenix.real_space_refine on Fri Mar 15 06:24:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7i_0357/03_2024/6n7i_0357_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7i_0357/03_2024/6n7i_0357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7i_0357/03_2024/6n7i_0357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7i_0357/03_2024/6n7i_0357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7i_0357/03_2024/6n7i_0357_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7i_0357/03_2024/6n7i_0357_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 27 5.49 5 Mg 4 5.21 5 S 65 5.16 5 C 6701 2.51 5 N 1899 2.21 5 O 2137 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 "C GLU 435": "OE1" <-> "OE2" 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" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10833 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: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1861 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 236} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 134 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "T" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} 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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.10, per 1000 atoms: 0.56 Number of scatterers: 10833 At special positions: 0 Unit cell: (80.25, 120.91, 135.89, 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 65 16.00 P 27 15.00 Mg 4 11.99 O 2137 8.00 N 1899 7.00 C 6701 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: 3.93 Conformation dependent library (CDL) restraints added in 1.8 seconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 5 sheets defined 31.8% alpha, 13.6% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 318 through 330 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: 3.898A pdb=" N ILE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 385 removed outlier: 3.817A pdb=" N ASP A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 379 through 385' Processing helix chain 'A' and resid 405 through 414 removed outlier: 3.583A pdb=" N TYR A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' 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 270 through 280 removed outlier: 4.432A pdb=" N GLU B 273 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 275 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG B 276 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS B 278 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 removed outlier: 3.553A pdb=" N ASP B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 297' 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 378 through 386 removed outlier: 3.764A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 414 removed outlier: 3.523A pdb=" N ALA B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) 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 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'C' and resid 272 through 278 Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'C' and resid 320 through 331 removed outlier: 3.671A 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 352 through 357 Processing helix chain 'C' and resid 366 through 374 removed outlier: 3.573A pdb=" N ARG C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 removed outlier: 3.680A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 removed outlier: 3.623A pdb=" N ALA C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 430 removed outlier: 3.676A pdb=" N VAL C 430 " --> pdb=" O SER C 427 " (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 'C' and resid 491 through 494 No H-bonds generated for 'chain 'C' and resid 491 through 494' Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 319 through 330 removed outlier: 3.649A pdb=" N GLN D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN D 325 " --> pdb=" O PHE D 321 " (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 375 Processing helix chain 'D' and resid 377 through 385 removed outlier: 3.559A pdb=" N ASP D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.072A 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 427 through 429 No H-bonds generated for 'chain 'D' and resid 427 through 429' Processing helix chain 'D' and resid 440 through 456 removed outlier: 3.544A 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 'E' and resid 318 through 327 Processing helix chain 'E' and resid 348 through 357 removed outlier: 3.763A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 371 removed outlier: 3.968A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 385 removed outlier: 3.663A pdb=" N GLU E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 413 Processing helix chain 'E' and resid 440 through 456 removed outlier: 3.836A 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 'F' and resid 274 through 279 Processing sheet with id= A, first strand: chain 'A' and resid 542 through 544 removed outlier: 7.050A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.381A 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: 6.947A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 498 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B 312 " --> pdb=" O CYS B 464 " (cutoff:3.500A) removed outlier: 3.743A 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: 6.823A pdb=" N VAL C 516 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR C 532 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 514 " --> pdb=" O TYR C 532 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 460 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL C 310 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 6.677A 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: 7.122A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 498 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 543 through 545 removed outlier: 4.313A pdb=" N TYR E 532 " --> pdb=" O SER E 545 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR E 498 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU E 502 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU E 460 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL E 310 " --> pdb=" O LEU E 460 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL E 462 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N SER E 312 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N CYS E 464 " --> pdb=" O SER E 312 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 4.32 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: 1810 1.31 - 1.43: 2714 1.43 - 1.56: 6301 1.56 - 1.69: 49 1.69 - 1.81: 110 Bond restraints: 10984 Sorted by residual: bond pdb=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.430 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C6 TTP C 700 " pdb=" N1 TTP C 700 " ideal model delta sigma weight residual 1.337 1.429 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C2 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.410 1.485 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 10979 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.15: 225 106.15 - 113.10: 5963 113.10 - 120.05: 3946 120.05 - 127.00: 4584 127.00 - 133.95: 107 Bond angle restraints: 14825 Sorted by residual: angle pdb=" N LYS D 318 " pdb=" CA LYS D 318 " pdb=" C LYS D 318 " ideal model delta sigma weight residual 112.68 103.19 9.49 1.33e+00 5.65e-01 5.09e+01 angle pdb=" C LEU A 288 " pdb=" CA LEU A 288 " pdb=" CB LEU A 288 " ideal model delta sigma weight residual 109.84 101.69 8.15 1.63e+00 3.76e-01 2.50e+01 angle pdb=" PA TTP D 700 " pdb=" O3A TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sigma weight residual 120.50 133.69 -13.19 3.00e+00 1.11e-01 1.93e+01 angle pdb=" PA TTP B 700 " pdb=" O3A TTP B 700 " pdb=" PB TTP B 700 " ideal model delta sigma weight residual 120.50 133.20 -12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" PA TTP E 700 " pdb=" O3A TTP E 700 " pdb=" PB TTP E 700 " ideal model delta sigma weight residual 120.50 132.39 -11.89 3.00e+00 1.11e-01 1.57e+01 ... (remaining 14820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 6410 35.51 - 71.03: 125 71.03 - 106.54: 10 106.54 - 142.06: 3 142.06 - 177.57: 6 Dihedral angle restraints: 6554 sinusoidal: 2795 harmonic: 3759 Sorted by residual: dihedral pdb=" O2G TTP D 700 " pdb=" O3B TTP D 700 " pdb=" PG TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sinusoidal sigma weight residual -180.00 -2.43 -177.57 1 2.00e+01 2.50e-03 4.80e+01 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 -6.25 -173.75 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 -58.32 101.51 -159.82 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 6551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1401 0.071 - 0.142: 260 0.142 - 0.214: 22 0.214 - 0.285: 4 0.285 - 0.356: 1 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CA ASN B 388 " pdb=" N ASN B 388 " pdb=" C ASN B 388 " pdb=" CB ASN B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+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 -2.77 0.26 2.00e-01 2.50e+01 1.65e+00 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 -2.76 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1685 not shown) Planarity restraints: 1822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 413 " 0.918 9.50e-02 1.11e+02 4.12e-01 1.03e+02 pdb=" NE ARG D 413 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG D 413 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 413 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 413 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 504 " 0.828 9.50e-02 1.11e+02 3.71e-01 8.37e+01 pdb=" NE ARG A 504 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG A 504 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 504 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 504 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 276 " -0.736 9.50e-02 1.11e+02 3.30e-01 6.63e+01 pdb=" NE ARG A 276 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 276 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 276 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 276 " -0.022 2.00e-02 2.50e+03 ... (remaining 1819 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 253 2.71 - 3.25: 9525 3.25 - 3.80: 16322 3.80 - 4.35: 21811 4.35 - 4.90: 36506 Nonbonded interactions: 84417 Sorted by model distance: nonbonded pdb=" NE2 GLN C 343 " pdb="MG MG C 701 " model vdw 2.157 2.250 nonbonded pdb=" O1B TTP B 700 " pdb="MG MG B 701 " model vdw 2.185 2.170 nonbonded pdb=" O1G TTP B 700 " pdb="MG MG B 701 " model vdw 2.200 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.223 2.170 nonbonded pdb=" O2B TTP E 700 " pdb="MG MG E 701 " model vdw 2.223 2.170 ... (remaining 84412 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 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 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 through 545)) selection = (chain 'B' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 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 through 545)) selection = (chain 'C' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 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 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 through 506 or resid 510 through 545)) selection = (chain 'E' and (resid 285 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.920 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.770 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 0.093 10984 Z= 0.314 Angle : 0.911 13.186 14825 Z= 0.488 Chirality : 0.055 0.356 1688 Planarity : 0.017 0.412 1822 Dihedral : 14.815 177.571 4148 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.53 % Allowed : 4.58 % Favored : 94.89 % 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: -3.45 (0.19), residues: 1308 helix: -2.86 (0.17), residues: 432 sheet: -0.33 (0.35), residues: 254 loop : -2.71 (0.20), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 381 HIS 0.009 0.001 HIS B 425 PHE 0.011 0.002 PHE D 523 TYR 0.007 0.001 TYR A 547 ARG 0.007 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 319 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: A 341 MET cc_start: 0.7360 (mmt) cc_final: 0.7118 (mmt) REVERT: A 513 LEU cc_start: 0.7069 (tp) cc_final: 0.6772 (tp) REVERT: B 408 LYS cc_start: 0.7905 (mttp) cc_final: 0.7683 (mmmt) REVERT: E 470 ASP cc_start: 0.5859 (p0) cc_final: 0.5578 (m-30) REVERT: E 532 TYR cc_start: 0.7350 (m-80) cc_final: 0.7149 (m-80) outliers start: 6 outliers final: 0 residues processed: 321 average time/residue: 0.2873 time to fit residues: 120.6475 Evaluate side-chains 145 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 475 HIS A 512 ASN B 357 HIS B 536 ASN C 324 GLN C 358 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS D 325 GLN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10984 Z= 0.283 Angle : 0.637 8.776 14825 Z= 0.313 Chirality : 0.045 0.156 1688 Planarity : 0.004 0.043 1822 Dihedral : 15.943 161.164 1642 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.17 % Allowed : 9.60 % Favored : 87.22 % 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: -2.20 (0.21), residues: 1308 helix: -1.13 (0.22), residues: 444 sheet: -0.24 (0.33), residues: 252 loop : -2.23 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 541 HIS 0.007 0.002 HIS A 357 PHE 0.021 0.002 PHE D 452 TYR 0.019 0.001 TYR D 411 ARG 0.007 0.001 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 380 GLN cc_start: 0.6889 (mt0) cc_final: 0.6183 (mt0) REVERT: B 444 ASN cc_start: 0.8381 (t0) cc_final: 0.8073 (t0) REVERT: D 316 MET cc_start: 0.7800 (mmp) cc_final: 0.7560 (mmp) outliers start: 36 outliers final: 21 residues processed: 184 average time/residue: 0.2424 time to fit residues: 61.8819 Evaluate side-chains 151 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 482 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10984 Z= 0.294 Angle : 0.615 7.974 14825 Z= 0.305 Chirality : 0.044 0.144 1688 Planarity : 0.004 0.040 1822 Dihedral : 15.829 160.151 1642 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.79 % Allowed : 11.10 % Favored : 85.11 % 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: -1.79 (0.22), residues: 1308 helix: -0.71 (0.23), residues: 458 sheet: -0.23 (0.33), residues: 251 loop : -1.97 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 381 HIS 0.007 0.002 HIS D 475 PHE 0.020 0.002 PHE E 523 TYR 0.017 0.001 TYR D 411 ARG 0.006 0.001 ARG F 276 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 131 time to evaluate : 1.196 Fit side-chains REVERT: A 316 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6622 (mpp) REVERT: A 380 GLN cc_start: 0.6677 (mt0) cc_final: 0.6347 (mt0) REVERT: A 386 PHE cc_start: 0.6903 (m-80) cc_final: 0.6640 (m-80) REVERT: A 505 ASN cc_start: 0.5572 (t0) cc_final: 0.5364 (t0) REVERT: D 509 ASP cc_start: 0.6276 (OUTLIER) cc_final: 0.5826 (p0) outliers start: 43 outliers final: 33 residues processed: 163 average time/residue: 0.2185 time to fit residues: 51.1387 Evaluate side-chains 160 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 129 optimal weight: 0.0980 chunk 115 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS A 444 ASN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10984 Z= 0.320 Angle : 0.630 8.317 14825 Z= 0.311 Chirality : 0.045 0.147 1688 Planarity : 0.003 0.043 1822 Dihedral : 15.823 159.795 1642 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.41 % Allowed : 12.51 % Favored : 83.08 % 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: -1.60 (0.22), residues: 1308 helix: -0.51 (0.24), residues: 452 sheet: -0.20 (0.33), residues: 251 loop : -1.84 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 381 HIS 0.007 0.001 HIS D 475 PHE 0.019 0.002 PHE E 523 TYR 0.017 0.001 TYR D 411 ARG 0.006 0.001 ARG F 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 133 time to evaluate : 1.033 Fit side-chains REVERT: A 316 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6742 (mpp) REVERT: A 386 PHE cc_start: 0.7009 (m-80) cc_final: 0.6660 (m-80) REVERT: D 509 ASP cc_start: 0.6165 (OUTLIER) cc_final: 0.5713 (p0) REVERT: E 368 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7806 (tt) REVERT: E 385 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6735 (tp) outliers start: 50 outliers final: 40 residues processed: 168 average time/residue: 0.2127 time to fit residues: 51.9674 Evaluate side-chains 169 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 125 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 0.0270 chunk 110 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS B 465 HIS ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN E 425 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10984 Z= 0.144 Angle : 0.506 7.899 14825 Z= 0.252 Chirality : 0.041 0.131 1688 Planarity : 0.002 0.039 1822 Dihedral : 15.251 157.603 1642 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.35 % Allowed : 14.54 % Favored : 82.11 % 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: -1.11 (0.23), residues: 1308 helix: -0.02 (0.25), residues: 453 sheet: 0.05 (0.33), residues: 252 loop : -1.62 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 381 HIS 0.004 0.001 HIS C 425 PHE 0.018 0.001 PHE C 452 TYR 0.015 0.001 TYR D 411 ARG 0.004 0.000 ARG F 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 143 time to evaluate : 1.160 Fit side-chains REVERT: A 316 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6667 (mpp) REVERT: A 386 PHE cc_start: 0.6784 (m-80) cc_final: 0.6513 (m-80) REVERT: B 273 GLU cc_start: 0.7570 (tp30) cc_final: 0.7361 (mm-30) REVERT: D 341 MET cc_start: 0.7855 (mmt) cc_final: 0.7560 (mmt) REVERT: D 452 PHE cc_start: 0.8492 (t80) cc_final: 0.8234 (t80) REVERT: E 368 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7649 (tt) REVERT: E 385 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6666 (tp) REVERT: E 510 MET cc_start: 0.6844 (ptp) cc_final: 0.6320 (mtp) outliers start: 38 outliers final: 20 residues processed: 171 average time/residue: 0.2319 time to fit residues: 55.5767 Evaluate side-chains 151 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 124 optimal weight: 0.5980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 425 HIS ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10984 Z= 0.154 Angle : 0.510 8.613 14825 Z= 0.253 Chirality : 0.041 0.130 1688 Planarity : 0.002 0.040 1822 Dihedral : 15.037 158.557 1642 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.44 % Allowed : 14.45 % Favored : 82.11 % 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: -0.80 (0.23), residues: 1308 helix: 0.33 (0.25), residues: 445 sheet: 0.13 (0.33), residues: 262 loop : -1.49 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 381 HIS 0.004 0.001 HIS C 425 PHE 0.013 0.001 PHE A 378 TYR 0.014 0.001 TYR D 411 ARG 0.008 0.000 ARG F 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 134 time to evaluate : 1.129 Fit side-chains REVERT: A 316 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6613 (mpp) REVERT: A 378 PHE cc_start: 0.6297 (t80) cc_final: 0.6035 (t80) REVERT: A 386 PHE cc_start: 0.6766 (m-80) cc_final: 0.6475 (m-80) REVERT: D 452 PHE cc_start: 0.8516 (t80) cc_final: 0.8241 (t80) REVERT: E 316 MET cc_start: 0.8166 (mmm) cc_final: 0.7861 (mmm) REVERT: E 368 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7599 (tt) REVERT: E 385 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6689 (tp) outliers start: 39 outliers final: 32 residues processed: 163 average time/residue: 0.2222 time to fit residues: 52.2173 Evaluate side-chains 162 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 516 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 425 HIS E 425 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10984 Z= 0.169 Angle : 0.526 9.025 14825 Z= 0.260 Chirality : 0.042 0.130 1688 Planarity : 0.002 0.039 1822 Dihedral : 14.938 158.000 1642 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.70 % Allowed : 14.63 % Favored : 81.67 % 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: -0.58 (0.24), residues: 1308 helix: 0.50 (0.26), residues: 438 sheet: 0.24 (0.33), residues: 260 loop : -1.31 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 381 HIS 0.004 0.001 HIS C 425 PHE 0.013 0.001 PHE C 321 TYR 0.014 0.001 TYR D 411 ARG 0.007 0.000 ARG F 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 1.291 Fit side-chains REVERT: A 316 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6714 (mpp) REVERT: B 328 GLN cc_start: 0.7300 (tp40) cc_final: 0.7064 (tp40) REVERT: D 452 PHE cc_start: 0.8480 (t80) cc_final: 0.8237 (t80) REVERT: E 368 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7633 (tt) REVERT: E 385 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6696 (tp) REVERT: E 510 MET cc_start: 0.6809 (ptp) cc_final: 0.6366 (mtp) outliers start: 42 outliers final: 33 residues processed: 161 average time/residue: 0.2214 time to fit residues: 51.2925 Evaluate side-chains 160 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 124 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 516 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 465 HIS ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10984 Z= 0.335 Angle : 0.644 11.368 14825 Z= 0.315 Chirality : 0.045 0.177 1688 Planarity : 0.003 0.039 1822 Dihedral : 15.460 159.018 1642 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.14 % Allowed : 14.45 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.23), residues: 1308 helix: 0.11 (0.25), residues: 450 sheet: 0.09 (0.33), residues: 258 loop : -1.39 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 381 HIS 0.007 0.001 HIS D 475 PHE 0.015 0.002 PHE C 321 TYR 0.015 0.001 TYR D 411 ARG 0.009 0.001 ARG F 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 121 time to evaluate : 1.244 Fit side-chains REVERT: A 316 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6839 (mpp) REVERT: A 386 PHE cc_start: 0.6946 (m-80) cc_final: 0.6600 (m-80) REVERT: A 533 MET cc_start: 0.7769 (mtp) cc_final: 0.7516 (mtm) REVERT: B 328 GLN cc_start: 0.7402 (tp40) cc_final: 0.7179 (tp40) REVERT: D 452 PHE cc_start: 0.8495 (t80) cc_final: 0.8183 (t80) REVERT: E 368 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7742 (tt) REVERT: E 385 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6837 (tp) outliers start: 47 outliers final: 37 residues processed: 155 average time/residue: 0.2162 time to fit residues: 48.3264 Evaluate side-chains 163 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 425 HIS Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 516 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 425 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10984 Z= 0.176 Angle : 0.553 11.236 14825 Z= 0.270 Chirality : 0.042 0.132 1688 Planarity : 0.002 0.038 1822 Dihedral : 15.104 156.833 1642 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.96 % Allowed : 14.63 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1308 helix: 0.36 (0.25), residues: 451 sheet: 0.21 (0.33), residues: 259 loop : -1.31 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 381 HIS 0.004 0.001 HIS C 425 PHE 0.013 0.001 PHE C 321 TYR 0.015 0.001 TYR A 394 ARG 0.007 0.000 ARG F 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 131 time to evaluate : 1.259 Fit side-chains REVERT: A 316 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6873 (mpp) REVERT: A 386 PHE cc_start: 0.6890 (m-80) cc_final: 0.6557 (m-80) REVERT: B 328 GLN cc_start: 0.7313 (tp40) cc_final: 0.7093 (tp40) REVERT: D 416 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8225 (mm) REVERT: D 452 PHE cc_start: 0.8469 (t80) cc_final: 0.8167 (t80) REVERT: E 368 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7642 (tt) REVERT: E 385 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6719 (tp) REVERT: E 446 MET cc_start: 0.6577 (mmt) cc_final: 0.5777 (tpt) REVERT: E 510 MET cc_start: 0.6749 (ptp) cc_final: 0.6376 (mtp) outliers start: 45 outliers final: 32 residues processed: 162 average time/residue: 0.2212 time to fit residues: 51.7510 Evaluate side-chains 163 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 0.0980 chunk 84 optimal weight: 0.0370 chunk 113 optimal weight: 6.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 425 HIS ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10984 Z= 0.136 Angle : 0.518 11.565 14825 Z= 0.255 Chirality : 0.041 0.131 1688 Planarity : 0.002 0.040 1822 Dihedral : 14.746 156.720 1642 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.91 % Allowed : 15.77 % 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: -0.42 (0.24), residues: 1308 helix: 0.64 (0.26), residues: 445 sheet: 0.34 (0.33), residues: 267 loop : -1.26 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 381 HIS 0.004 0.001 HIS C 425 PHE 0.011 0.001 PHE C 321 TYR 0.015 0.001 TYR A 394 ARG 0.007 0.000 ARG F 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 1.250 Fit side-chains REVERT: A 316 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6857 (mpp) REVERT: A 386 PHE cc_start: 0.6843 (m-80) cc_final: 0.6536 (m-80) REVERT: D 341 MET cc_start: 0.7328 (mmp) cc_final: 0.6986 (mmp) REVERT: D 416 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8200 (mm) REVERT: E 368 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7675 (tt) REVERT: E 385 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6669 (tp) REVERT: E 446 MET cc_start: 0.6488 (mmt) cc_final: 0.5702 (tpt) REVERT: E 510 MET cc_start: 0.6739 (ptp) cc_final: 0.6366 (mtp) outliers start: 33 outliers final: 25 residues processed: 158 average time/residue: 0.2317 time to fit residues: 51.8611 Evaluate side-chains 152 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 0.0370 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 425 HIS ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.159229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135869 restraints weight = 14534.327| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.59 r_work: 0.3660 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10984 Z= 0.232 Angle : 0.586 11.257 14825 Z= 0.287 Chirality : 0.043 0.131 1688 Planarity : 0.003 0.037 1822 Dihedral : 15.022 158.456 1642 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.17 % Allowed : 15.95 % Favored : 80.88 % 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: -0.47 (0.24), residues: 1308 helix: 0.50 (0.25), residues: 443 sheet: 0.30 (0.33), residues: 259 loop : -1.18 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 381 HIS 0.008 0.001 HIS B 425 PHE 0.013 0.001 PHE C 321 TYR 0.014 0.001 TYR A 394 ARG 0.007 0.000 ARG F 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.42 seconds wall clock time: 43 minutes 52.27 seconds (2632.27 seconds total)