Starting phenix.real_space_refine (version: dev) on Sun Feb 19 22:43:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7i_0357/02_2023/6n7i_0357_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7i_0357/02_2023/6n7i_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_0357/02_2023/6n7i_0357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7i_0357/02_2023/6n7i_0357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7i_0357/02_2023/6n7i_0357_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7i_0357/02_2023/6n7i_0357_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 6.63, per 1000 atoms: 0.61 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: 4.19 Conformation dependent library (CDL) restraints added in 1.6 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: 3.46 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: 2.91 Time building geometry restraints manager: 4.59 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 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. 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: 0.980 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: 4.770 Check model and map are aligned: 0.180 Process input model: 32.540 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 % 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 *********************** 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 : 1.357 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 321 average time/residue: 0.3035 time to fit residues: 127.7750 Evaluate side-chains 143 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7616 ------------------------------------------------------------------------------- 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: 3.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 465 HIS 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 C 536 ASN D 325 GLN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 10984 Z= 0.365 Angle : 0.695 9.567 14825 Z= 0.342 Chirality : 0.047 0.181 1688 Planarity : 0.004 0.043 1822 Dihedral : 16.080 161.386 1642 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 3.52 % 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: -2.33 (0.21), residues: 1308 helix: -1.27 (0.22), residues: 444 sheet: -0.37 (0.33), residues: 252 loop : -2.26 (0.22), residues: 612 *********************** 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: 40 poor density : 151 time to evaluate : 1.454 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 25 residues processed: 183 average time/residue: 0.2536 time to fit residues: 64.6338 Evaluate side-chains 150 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1117 time to fit residues: 6.8069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.0040 chunk 37 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 425 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3101 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= 0.159 Angle : 0.531 7.242 14825 Z= 0.265 Chirality : 0.042 0.136 1688 Planarity : 0.003 0.039 1822 Dihedral : 15.534 158.892 1642 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 2.11 % 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: -1.64 (0.22), residues: 1308 helix: -0.47 (0.24), residues: 442 sheet: -0.14 (0.34), residues: 252 loop : -1.97 (0.23), residues: 614 *********************** 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 169 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 1.210 Fit side-chains outliers start: 24 outliers final: 9 residues processed: 158 average time/residue: 0.2555 time to fit residues: 56.8182 Evaluate side-chains 137 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1137 time to fit residues: 3.5486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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** B 507 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.075 10984 Z= 0.444 Angle : 0.725 8.962 14825 Z= 0.357 Chirality : 0.048 0.193 1688 Planarity : 0.004 0.063 1822 Dihedral : 16.091 160.329 1642 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.22), residues: 1308 helix: -0.67 (0.23), residues: 451 sheet: -0.29 (0.33), residues: 249 loop : -1.82 (0.24), residues: 608 *********************** 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 153 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.296 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 143 average time/residue: 0.2237 time to fit residues: 46.6357 Evaluate side-chains 136 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1013 time to fit residues: 5.0091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 0.0870 chunk 110 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.0050 chunk 116 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 0.4372 ------------------------------------------------------------------------------- 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** B 507 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3691 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= 0.133 Angle : 0.516 7.939 14825 Z= 0.257 Chirality : 0.041 0.130 1688 Planarity : 0.002 0.043 1822 Dihedral : 15.272 157.637 1642 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.88 % 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: -1.12 (0.23), residues: 1308 helix: -0.01 (0.25), residues: 452 sheet: -0.07 (0.33), residues: 253 loop : -1.60 (0.24), residues: 603 *********************** 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 150 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.222 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 146 average time/residue: 0.2438 time to fit residues: 50.5425 Evaluate side-chains 123 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0978 time to fit residues: 2.4887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 129 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3827 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= 0.158 Angle : 0.540 11.176 14825 Z= 0.263 Chirality : 0.042 0.133 1688 Planarity : 0.002 0.044 1822 Dihedral : 15.101 159.313 1642 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 1.15 % 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: -0.82 (0.23), residues: 1308 helix: 0.26 (0.25), residues: 446 sheet: 0.14 (0.34), residues: 251 loop : -1.43 (0.25), residues: 611 *********************** 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 139 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.282 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 136 average time/residue: 0.2494 time to fit residues: 48.5004 Evaluate side-chains 130 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1049 time to fit residues: 3.1014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10984 Z= 0.201 Angle : 0.569 10.410 14825 Z= 0.278 Chirality : 0.042 0.134 1688 Planarity : 0.003 0.039 1822 Dihedral : 15.153 159.149 1642 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 1.15 % 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: -0.72 (0.23), residues: 1308 helix: 0.30 (0.25), residues: 446 sheet: 0.18 (0.34), residues: 250 loop : -1.33 (0.25), residues: 612 *********************** 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 136 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.178 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 128 average time/residue: 0.2413 time to fit residues: 44.4973 Evaluate side-chains 125 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1036 time to fit residues: 3.1307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 10984 Z= 0.398 Angle : 0.712 10.078 14825 Z= 0.348 Chirality : 0.047 0.166 1688 Planarity : 0.004 0.054 1822 Dihedral : 15.818 160.270 1642 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.97 % 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: -1.15 (0.23), residues: 1308 helix: -0.08 (0.24), residues: 447 sheet: -0.20 (0.32), residues: 262 loop : -1.52 (0.25), residues: 599 *********************** 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 126 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.834 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 121 average time/residue: 0.2580 time to fit residues: 44.6505 Evaluate side-chains 121 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1059 time to fit residues: 3.6031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4186 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= 0.188 Angle : 0.574 11.667 14825 Z= 0.281 Chirality : 0.042 0.137 1688 Planarity : 0.003 0.038 1822 Dihedral : 15.339 158.089 1642 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1308 helix: 0.24 (0.25), residues: 448 sheet: 0.01 (0.33), residues: 259 loop : -1.40 (0.25), residues: 601 *********************** 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 124 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.472 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 122 average time/residue: 0.2548 time to fit residues: 43.8103 Evaluate side-chains 116 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0971 time to fit residues: 1.8316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 10984 Z= 0.302 Angle : 0.646 11.497 14825 Z= 0.315 Chirality : 0.045 0.141 1688 Planarity : 0.003 0.037 1822 Dihedral : 15.591 160.016 1642 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 0.62 % 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: -0.97 (0.23), residues: 1308 helix: 0.14 (0.25), residues: 448 sheet: -0.05 (0.33), residues: 262 loop : -1.50 (0.25), residues: 598 ********************** 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 122 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.304 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 119 average time/residue: 0.2555 time to fit residues: 43.3933 Evaluate side-chains 114 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1192 time to fit residues: 1.9134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 109 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.158571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135323 restraints weight = 14536.562| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.59 r_work: 0.3646 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10984 Z= 0.207 Angle : 0.589 11.962 14825 Z= 0.287 Chirality : 0.043 0.150 1688 Planarity : 0.003 0.039 1822 Dihedral : 15.339 158.232 1642 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.23), residues: 1308 helix: 0.35 (0.25), residues: 447 sheet: 0.09 (0.33), residues: 252 loop : -1.39 (0.25), residues: 609 =============================================================================== Job complete usr+sys time: 2322.44 seconds wall clock time: 43 minutes 35.23 seconds (2615.23 seconds total)