Starting phenix.real_space_refine on Wed Sep 25 22:34:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xuh_33469/09_2024/7xuh_33469.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xuh_33469/09_2024/7xuh_33469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xuh_33469/09_2024/7xuh_33469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xuh_33469/09_2024/7xuh_33469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xuh_33469/09_2024/7xuh_33469.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xuh_33469/09_2024/7xuh_33469.cif" } resolution = 2.76 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 7526 2.51 5 N 1812 2.21 5 O 1996 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11380 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5519 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 31, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 5519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5519 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 31, 'TRANS': 675} Chain breaks: 1 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'I2L': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'I2L': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 7.39, per 1000 atoms: 0.65 Number of scatterers: 11380 At special positions: 0 Unit cell: (98.917, 122.831, 115.222, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 F 6 9.00 O 1996 8.00 N 1812 7.00 C 7526 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 - 3.00 Amino acid : True - 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: 2.67 Conformation dependent library (CDL) restraints added in 1.5 seconds 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 3 sheets defined 62.1% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.711A pdb=" N ASN A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 removed outlier: 4.177A pdb=" N HIS A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.950A pdb=" N LEU A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 95 removed outlier: 5.912A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.682A pdb=" N LEU A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 Processing helix chain 'A' and resid 170 through 196 removed outlier: 3.655A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.563A pdb=" N TYR A 204 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.535A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 230' Processing helix chain 'A' and resid 241 through 252 Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.717A pdb=" N THR A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 276 removed outlier: 3.738A pdb=" N THR A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.552A pdb=" N ILE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.564A pdb=" N PHE A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.797A pdb=" N ASN A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 366 removed outlier: 3.714A pdb=" N GLY A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.919A pdb=" N LEU A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.599A pdb=" N ALA A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 457 through 463 removed outlier: 3.838A pdb=" N ARG A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 483 removed outlier: 3.561A pdb=" N ILE A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.919A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 503 " --> pdb=" O ILE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 563 through 583 Processing helix chain 'A' and resid 612 through 616 removed outlier: 3.548A pdb=" N LEU A 616 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 removed outlier: 3.723A pdb=" N ILE A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.620A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 724 removed outlier: 3.569A pdb=" N MET A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 25 removed outlier: 3.710A pdb=" N ASN B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 43 removed outlier: 4.178A pdb=" N HIS B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.950A pdb=" N LEU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 68 through 95 removed outlier: 5.912A pdb=" N LEU B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 110 through 120 removed outlier: 3.681A pdb=" N LEU B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 145 Processing helix chain 'B' and resid 170 through 196 removed outlier: 3.656A pdb=" N VAL B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.563A pdb=" N TYR B 204 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 removed outlier: 3.500A pdb=" N VAL B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.535A pdb=" N ILE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 230' Processing helix chain 'B' and resid 241 through 252 Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.717A pdb=" N THR B 257 " --> pdb=" O ILE B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 276 removed outlier: 3.738A pdb=" N THR B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.552A pdb=" N ILE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.563A pdb=" N PHE B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.797A pdb=" N ASN B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 366 removed outlier: 3.714A pdb=" N GLY B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 removed outlier: 3.919A pdb=" N LEU B 375 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.599A pdb=" N ALA B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 457 through 463 removed outlier: 3.837A pdb=" N ARG B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 483 removed outlier: 3.561A pdb=" N ILE B 471 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 503 removed outlier: 3.919A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 499 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 503 " --> pdb=" O ILE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 563 through 583 Processing helix chain 'B' and resid 612 through 616 removed outlier: 3.548A pdb=" N LEU B 616 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 677 removed outlier: 3.723A pdb=" N ILE B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 removed outlier: 3.619A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 724 removed outlier: 3.570A pdb=" N MET B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.773A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 13.002A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS A 536 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP A 652 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE A 538 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.773A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 13.002A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS B 536 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASP B 652 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE B 538 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE B 710 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE B 683 " --> pdb=" O PHE B 710 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 1782 1.26 - 1.40: 2762 1.40 - 1.54: 6601 1.54 - 1.67: 435 1.67 - 1.81: 62 Bond restraints: 11642 Sorted by residual: bond pdb=" C13 I2L A1001 " pdb=" C17 I2L A1001 " ideal model delta sigma weight residual 1.457 1.780 -0.323 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C13 I2L B 803 " pdb=" C17 I2L B 803 " ideal model delta sigma weight residual 1.457 1.779 -0.322 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C14 I2L B 803 " pdb=" C16 I2L B 803 " ideal model delta sigma weight residual 1.397 1.126 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C14 I2L A1001 " pdb=" C16 I2L A1001 " ideal model delta sigma weight residual 1.397 1.126 0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C10 I2L A1001 " pdb=" C12 I2L A1001 " ideal model delta sigma weight residual 1.397 1.602 -0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 11637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 15313 2.25 - 4.50: 450 4.50 - 6.74: 59 6.74 - 8.99: 22 8.99 - 11.24: 8 Bond angle restraints: 15852 Sorted by residual: angle pdb=" CA VAL A 288 " pdb=" CB VAL A 288 " pdb=" CG1 VAL A 288 " ideal model delta sigma weight residual 110.40 117.60 -7.20 1.70e+00 3.46e-01 1.80e+01 angle pdb=" CA VAL B 288 " pdb=" CB VAL B 288 " pdb=" CG1 VAL B 288 " ideal model delta sigma weight residual 110.40 117.59 -7.19 1.70e+00 3.46e-01 1.79e+01 angle pdb=" C PRO A 150 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C PRO B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 129.06 -7.52 1.91e+00 2.74e-01 1.55e+01 angle pdb=" C VAL A 241 " pdb=" N SER A 242 " pdb=" CA SER A 242 " ideal model delta sigma weight residual 120.38 126.01 -5.63 1.46e+00 4.69e-01 1.49e+01 ... (remaining 15847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 6958 23.98 - 47.96: 338 47.96 - 71.94: 38 71.94 - 95.92: 20 95.92 - 119.90: 2 Dihedral angle restraints: 7356 sinusoidal: 3258 harmonic: 4098 Sorted by residual: dihedral pdb=" CA PRO B 150 " pdb=" C PRO B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta harmonic sigma weight residual 180.00 -139.35 -40.65 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CA PRO A 150 " pdb=" C PRO A 150 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta harmonic sigma weight residual 180.00 -139.40 -40.60 0 5.00e+00 4.00e-02 6.59e+01 dihedral pdb=" CA ASP A 239 " pdb=" C ASP A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta harmonic sigma weight residual 180.00 152.28 27.72 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 7353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1175 0.046 - 0.091: 535 0.091 - 0.136: 145 0.136 - 0.182: 19 0.182 - 0.227: 10 Chirality restraints: 1884 Sorted by residual: chirality pdb=" CB VAL A 560 " pdb=" CA VAL A 560 " pdb=" CG1 VAL A 560 " pdb=" CG2 VAL A 560 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL B 560 " pdb=" CA VAL B 560 " pdb=" CG1 VAL B 560 " pdb=" CG2 VAL B 560 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE B 677 " pdb=" CA ILE B 677 " pdb=" CG1 ILE B 677 " pdb=" CG2 ILE B 677 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1881 not shown) Planarity restraints: 1934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 433 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO A 434 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 434 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 434 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 433 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO B 434 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 434 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 434 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 18 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C THR A 18 " 0.046 2.00e-02 2.50e+03 pdb=" O THR A 18 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN A 19 " -0.016 2.00e-02 2.50e+03 ... (remaining 1931 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2975 2.80 - 3.32: 9741 3.32 - 3.85: 17679 3.85 - 4.37: 21162 4.37 - 4.90: 36354 Nonbonded interactions: 87911 Sorted by model distance: nonbonded pdb=" OG1 THR A 121 " pdb=" OE2 GLU A 374 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR B 121 " pdb=" OE2 GLU B 374 " model vdw 2.275 3.040 nonbonded pdb=" NZ LYS B 245 " pdb=" OAH Y01 B 804 " model vdw 2.293 3.120 nonbonded pdb=" NZ LYS A 245 " pdb=" OAH Y01 A1002 " model vdw 2.294 3.120 nonbonded pdb=" OG1 THR B 712 " pdb=" OD2 ASP B 715 " model vdw 2.300 3.040 ... (remaining 87906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 725 or resid 1002 or resid 1004 through 1005)) selection = (chain 'B' and (resid 8 through 725 or resid 802 or resid 804 through 805)) } 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: 7.080 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.910 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.323 11642 Z= 0.713 Angle : 0.962 11.241 15852 Z= 0.505 Chirality : 0.055 0.227 1884 Planarity : 0.008 0.068 1934 Dihedral : 14.395 119.898 4708 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.98 % Allowed : 5.74 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.53 (0.17), residues: 1406 helix: -2.22 (0.13), residues: 828 sheet: 1.32 (0.72), residues: 34 loop : -2.61 (0.22), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 63 HIS 0.004 0.001 HIS A 647 PHE 0.031 0.002 PHE A 130 TYR 0.029 0.002 TYR B 9 ARG 0.006 0.001 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.188 Fit side-chains REVERT: A 34 THR cc_start: 0.6038 (OUTLIER) cc_final: 0.5818 (m) REVERT: A 171 ASP cc_start: 0.8246 (p0) cc_final: 0.7971 (p0) REVERT: A 193 PHE cc_start: 0.8937 (m-80) cc_final: 0.8656 (m-80) REVERT: A 296 MET cc_start: 0.8812 (mmm) cc_final: 0.8603 (mmp) REVERT: A 558 ASP cc_start: 0.7042 (m-30) cc_final: 0.6824 (m-30) REVERT: B 34 THR cc_start: 0.6079 (OUTLIER) cc_final: 0.5846 (m) REVERT: B 171 ASP cc_start: 0.8232 (p0) cc_final: 0.7943 (p0) REVERT: B 193 PHE cc_start: 0.8939 (m-80) cc_final: 0.8668 (m-80) REVERT: B 296 MET cc_start: 0.8768 (mmm) cc_final: 0.8562 (mmp) REVERT: B 558 ASP cc_start: 0.6989 (m-30) cc_final: 0.6723 (m-30) outliers start: 12 outliers final: 6 residues processed: 145 average time/residue: 1.2109 time to fit residues: 190.4502 Evaluate side-chains 86 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 406 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 58 optimal weight: 0.0270 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.0980 chunk 81 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 495 GLN A 513 ASN B 337 GLN B 495 GLN B 504 GLN B 513 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11642 Z= 0.148 Angle : 0.567 8.247 15852 Z= 0.292 Chirality : 0.041 0.133 1884 Planarity : 0.005 0.045 1934 Dihedral : 8.069 79.582 2146 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.48 % Allowed : 10.00 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.17 (0.22), residues: 1406 helix: -0.19 (0.18), residues: 840 sheet: 2.72 (0.72), residues: 34 loop : -1.91 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 472 HIS 0.002 0.001 HIS A 38 PHE 0.017 0.001 PHE B 130 TYR 0.010 0.001 TYR A 9 ARG 0.009 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 1.265 Fit side-chains REVERT: A 58 PHE cc_start: 0.8053 (m-80) cc_final: 0.7512 (t80) REVERT: A 171 ASP cc_start: 0.8074 (p0) cc_final: 0.7762 (p0) REVERT: A 193 PHE cc_start: 0.8868 (m-80) cc_final: 0.8587 (m-80) REVERT: B 58 PHE cc_start: 0.8071 (m-80) cc_final: 0.7586 (t80) REVERT: B 193 PHE cc_start: 0.8846 (m-80) cc_final: 0.8566 (m-80) REVERT: B 274 ILE cc_start: 0.8636 (pt) cc_final: 0.8430 (pp) REVERT: B 285 LYS cc_start: 0.7502 (tmtt) cc_final: 0.7106 (tptt) outliers start: 18 outliers final: 8 residues processed: 110 average time/residue: 0.8689 time to fit residues: 107.2647 Evaluate side-chains 84 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 594 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN A 504 GLN B 436 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11642 Z= 0.208 Angle : 0.538 5.607 15852 Z= 0.280 Chirality : 0.041 0.129 1884 Planarity : 0.004 0.046 1934 Dihedral : 6.492 59.504 2138 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.62 % Allowed : 10.49 % Favored : 86.89 % 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: -0.35 (0.23), residues: 1406 helix: 0.51 (0.19), residues: 834 sheet: 3.26 (0.79), residues: 34 loop : -1.64 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 472 HIS 0.004 0.001 HIS A 714 PHE 0.019 0.001 PHE A 130 TYR 0.016 0.001 TYR B 9 ARG 0.005 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 85 time to evaluate : 1.208 Fit side-chains REVERT: A 58 PHE cc_start: 0.8203 (m-80) cc_final: 0.7783 (t80) REVERT: A 193 PHE cc_start: 0.8919 (m-80) cc_final: 0.8645 (m-80) REVERT: A 285 LYS cc_start: 0.7563 (tmtt) cc_final: 0.7241 (tmtm) REVERT: A 660 ASP cc_start: 0.8242 (p0) cc_final: 0.7914 (p0) REVERT: B 58 PHE cc_start: 0.8118 (m-80) cc_final: 0.7752 (t80) REVERT: B 171 ASP cc_start: 0.8137 (p0) cc_final: 0.7821 (p0) REVERT: B 193 PHE cc_start: 0.8927 (m-80) cc_final: 0.8647 (m-80) REVERT: B 285 LYS cc_start: 0.7574 (tmtt) cc_final: 0.7242 (tmtm) REVERT: B 660 ASP cc_start: 0.8346 (p0) cc_final: 0.8021 (p0) outliers start: 32 outliers final: 18 residues processed: 109 average time/residue: 0.9899 time to fit residues: 119.4592 Evaluate side-chains 96 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 HIS B 714 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11642 Z= 0.247 Angle : 0.544 6.971 15852 Z= 0.284 Chirality : 0.042 0.130 1884 Planarity : 0.004 0.049 1934 Dihedral : 6.302 58.437 2136 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.30 % Allowed : 12.30 % Favored : 85.41 % 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: -0.04 (0.23), residues: 1406 helix: 0.80 (0.19), residues: 832 sheet: 3.20 (0.80), residues: 34 loop : -1.56 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.005 0.001 HIS B 714 PHE 0.018 0.001 PHE A 130 TYR 0.017 0.001 TYR A 9 ARG 0.009 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 1.134 Fit side-chains REVERT: A 58 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7878 (t80) REVERT: A 171 ASP cc_start: 0.8180 (p0) cc_final: 0.7761 (p0) REVERT: A 193 PHE cc_start: 0.8934 (m-80) cc_final: 0.8632 (m-80) REVERT: A 281 ARG cc_start: 0.7393 (ttm110) cc_final: 0.6807 (ttm170) REVERT: A 285 LYS cc_start: 0.7595 (tmtt) cc_final: 0.7308 (tmtm) REVERT: A 660 ASP cc_start: 0.8297 (p0) cc_final: 0.8088 (p0) REVERT: B 58 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7907 (t80) REVERT: B 169 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8251 (tp) REVERT: B 193 PHE cc_start: 0.8936 (m-80) cc_final: 0.8635 (m-80) REVERT: B 281 ARG cc_start: 0.7372 (ttm110) cc_final: 0.6791 (ttm170) REVERT: B 285 LYS cc_start: 0.7624 (tmtt) cc_final: 0.7326 (tmtm) REVERT: B 660 ASP cc_start: 0.8312 (p0) cc_final: 0.7982 (p0) outliers start: 28 outliers final: 21 residues processed: 103 average time/residue: 0.9969 time to fit residues: 113.6286 Evaluate side-chains 101 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11642 Z= 0.259 Angle : 0.545 5.575 15852 Z= 0.285 Chirality : 0.042 0.129 1884 Planarity : 0.004 0.051 1934 Dihedral : 6.219 55.811 2136 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.70 % Allowed : 12.05 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.23), residues: 1406 helix: 0.90 (0.19), residues: 844 sheet: 3.02 (0.80), residues: 34 loop : -1.46 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 63 HIS 0.004 0.001 HIS B 647 PHE 0.018 0.001 PHE A 130 TYR 0.018 0.001 TYR A 9 ARG 0.007 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 83 time to evaluate : 1.283 Fit side-chains REVERT: A 58 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7906 (t80) REVERT: A 169 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8241 (tp) REVERT: A 193 PHE cc_start: 0.8942 (m-80) cc_final: 0.8658 (m-80) REVERT: A 281 ARG cc_start: 0.7391 (ttm110) cc_final: 0.6823 (ttm170) REVERT: A 285 LYS cc_start: 0.7620 (tmtt) cc_final: 0.7366 (tmtm) REVERT: A 637 LEU cc_start: 0.7721 (mm) cc_final: 0.7425 (tp) REVERT: A 660 ASP cc_start: 0.8341 (p0) cc_final: 0.7989 (p0) REVERT: B 58 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7882 (t80) REVERT: B 169 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8219 (tp) REVERT: B 171 ASP cc_start: 0.8303 (p0) cc_final: 0.7981 (p0) REVERT: B 193 PHE cc_start: 0.8944 (m-80) cc_final: 0.8649 (m-80) REVERT: B 637 LEU cc_start: 0.7780 (mm) cc_final: 0.7502 (tp) REVERT: B 660 ASP cc_start: 0.8356 (p0) cc_final: 0.8036 (p0) outliers start: 33 outliers final: 18 residues processed: 104 average time/residue: 1.0332 time to fit residues: 118.7610 Evaluate side-chains 100 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11642 Z= 0.232 Angle : 0.552 7.124 15852 Z= 0.286 Chirality : 0.041 0.128 1884 Planarity : 0.004 0.050 1934 Dihedral : 6.106 53.562 2136 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.79 % Allowed : 12.62 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1406 helix: 1.03 (0.19), residues: 846 sheet: 3.04 (0.80), residues: 34 loop : -1.39 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 63 HIS 0.004 0.001 HIS A 647 PHE 0.017 0.001 PHE A 130 TYR 0.016 0.001 TYR A 9 ARG 0.010 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 81 time to evaluate : 1.206 Fit side-chains REVERT: A 58 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7905 (t80) REVERT: A 169 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8167 (tp) REVERT: A 171 ASP cc_start: 0.8250 (p0) cc_final: 0.7895 (p0) REVERT: A 193 PHE cc_start: 0.8931 (m-80) cc_final: 0.8648 (m-80) REVERT: A 241 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7995 (t) REVERT: A 281 ARG cc_start: 0.7409 (ttm110) cc_final: 0.6832 (ttm170) REVERT: A 285 LYS cc_start: 0.7711 (tmtt) cc_final: 0.7487 (tmtm) REVERT: A 637 LEU cc_start: 0.7707 (mm) cc_final: 0.7434 (tp) REVERT: A 660 ASP cc_start: 0.8298 (p0) cc_final: 0.8097 (p0) REVERT: B 58 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7840 (t80) REVERT: B 169 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8227 (tp) REVERT: B 171 ASP cc_start: 0.8226 (p0) cc_final: 0.7845 (p0) REVERT: B 193 PHE cc_start: 0.8933 (m-80) cc_final: 0.8640 (m-80) REVERT: B 281 ARG cc_start: 0.7525 (ttm110) cc_final: 0.7177 (mtp-110) REVERT: B 637 LEU cc_start: 0.7708 (mm) cc_final: 0.7451 (tp) REVERT: B 660 ASP cc_start: 0.8330 (p0) cc_final: 0.7980 (p0) outliers start: 34 outliers final: 19 residues processed: 103 average time/residue: 1.0388 time to fit residues: 118.7381 Evaluate side-chains 100 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 0.0270 chunk 75 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11642 Z= 0.155 Angle : 0.510 6.212 15852 Z= 0.265 Chirality : 0.040 0.124 1884 Planarity : 0.004 0.046 1934 Dihedral : 5.704 48.911 2136 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.70 % Allowed : 13.11 % Favored : 84.18 % 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: 0.63 (0.23), residues: 1406 helix: 1.32 (0.19), residues: 834 sheet: 3.24 (0.81), residues: 34 loop : -1.23 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 63 HIS 0.002 0.001 HIS B 647 PHE 0.015 0.001 PHE A 130 TYR 0.010 0.001 TYR A 9 ARG 0.010 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 1.255 Fit side-chains REVERT: A 58 PHE cc_start: 0.8046 (m-80) cc_final: 0.7723 (t80) REVERT: A 169 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8176 (tp) REVERT: A 171 ASP cc_start: 0.8264 (p0) cc_final: 0.7855 (p0) REVERT: A 193 PHE cc_start: 0.8898 (m-80) cc_final: 0.8627 (m-80) REVERT: A 241 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7874 (t) REVERT: B 58 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7773 (t80) REVERT: B 193 PHE cc_start: 0.8898 (m-80) cc_final: 0.8631 (m-80) REVERT: B 241 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7883 (t) REVERT: B 281 ARG cc_start: 0.7466 (ttm110) cc_final: 0.7167 (mtp-110) outliers start: 33 outliers final: 17 residues processed: 105 average time/residue: 1.0379 time to fit residues: 121.1753 Evaluate side-chains 99 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.0570 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 0.2980 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11642 Z= 0.139 Angle : 0.504 7.720 15852 Z= 0.261 Chirality : 0.040 0.133 1884 Planarity : 0.004 0.043 1934 Dihedral : 5.425 43.604 2136 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.13 % Allowed : 14.10 % Favored : 83.77 % 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: 1406 helix: 1.47 (0.19), residues: 838 sheet: 3.37 (0.81), residues: 34 loop : -1.07 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 63 HIS 0.002 0.000 HIS A 220 PHE 0.015 0.001 PHE B 130 TYR 0.010 0.001 TYR A 545 ARG 0.010 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 86 time to evaluate : 1.585 Fit side-chains REVERT: A 43 CYS cc_start: 0.7672 (t) cc_final: 0.7230 (m) REVERT: A 58 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7720 (t80) REVERT: A 169 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8192 (tp) REVERT: A 171 ASP cc_start: 0.8209 (p0) cc_final: 0.7909 (p0) REVERT: A 193 PHE cc_start: 0.8877 (m-80) cc_final: 0.8637 (m-80) REVERT: A 281 ARG cc_start: 0.7401 (ttm110) cc_final: 0.6902 (ttm170) REVERT: A 609 ASP cc_start: 0.8478 (p0) cc_final: 0.8240 (p0) REVERT: B 58 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7739 (t80) REVERT: B 171 ASP cc_start: 0.8251 (p0) cc_final: 0.7893 (p0) REVERT: B 193 PHE cc_start: 0.8886 (m-80) cc_final: 0.8642 (m-80) REVERT: B 281 ARG cc_start: 0.7505 (ttm110) cc_final: 0.7222 (mtp-110) REVERT: B 609 ASP cc_start: 0.8390 (p0) cc_final: 0.8174 (p0) outliers start: 26 outliers final: 16 residues processed: 98 average time/residue: 1.1365 time to fit residues: 124.5723 Evaluate side-chains 104 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 504 GLN B 322 ASN B 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11642 Z= 0.218 Angle : 0.539 6.780 15852 Z= 0.282 Chirality : 0.041 0.131 1884 Planarity : 0.004 0.047 1934 Dihedral : 5.607 40.858 2136 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.89 % Allowed : 14.43 % Favored : 83.69 % 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: 1406 helix: 1.43 (0.19), residues: 840 sheet: 3.20 (0.79), residues: 34 loop : -1.13 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 63 HIS 0.004 0.001 HIS B 647 PHE 0.018 0.001 PHE A 130 TYR 0.015 0.001 TYR A 9 ARG 0.011 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 1.854 Fit side-chains REVERT: A 43 CYS cc_start: 0.7590 (t) cc_final: 0.7147 (m) REVERT: A 58 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7832 (t80) REVERT: A 193 PHE cc_start: 0.8908 (m-80) cc_final: 0.8646 (m-80) REVERT: A 241 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7962 (t) REVERT: A 281 ARG cc_start: 0.7383 (ttm110) cc_final: 0.6843 (ttm170) REVERT: A 609 ASP cc_start: 0.8496 (p0) cc_final: 0.8219 (p0) REVERT: B 58 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7863 (t80) REVERT: B 171 ASP cc_start: 0.8284 (p0) cc_final: 0.7929 (p0) REVERT: B 193 PHE cc_start: 0.8910 (m-80) cc_final: 0.8650 (m-80) REVERT: B 281 ARG cc_start: 0.7530 (ttm110) cc_final: 0.7221 (mtp-110) REVERT: B 609 ASP cc_start: 0.8471 (p0) cc_final: 0.8204 (p0) outliers start: 23 outliers final: 16 residues processed: 102 average time/residue: 1.0988 time to fit residues: 125.5910 Evaluate side-chains 104 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 chunk 139 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11642 Z= 0.178 Angle : 0.543 9.819 15852 Z= 0.279 Chirality : 0.041 0.140 1884 Planarity : 0.004 0.043 1934 Dihedral : 5.435 40.016 2136 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.72 % Allowed : 15.08 % Favored : 83.20 % 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: 0.91 (0.23), residues: 1406 helix: 1.52 (0.19), residues: 840 sheet: 3.35 (0.80), residues: 34 loop : -1.09 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 63 HIS 0.003 0.001 HIS A 647 PHE 0.016 0.001 PHE A 130 TYR 0.012 0.001 TYR A 9 ARG 0.011 0.000 ARG A 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 1.229 Fit side-chains REVERT: A 43 CYS cc_start: 0.7615 (t) cc_final: 0.7157 (m) REVERT: A 58 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7765 (t80) REVERT: A 171 ASP cc_start: 0.8280 (p0) cc_final: 0.7915 (p0) REVERT: A 193 PHE cc_start: 0.8905 (m-80) cc_final: 0.8645 (m-80) REVERT: A 241 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7875 (t) REVERT: A 281 ARG cc_start: 0.7441 (ttm110) cc_final: 0.6918 (ttm170) REVERT: A 609 ASP cc_start: 0.8520 (p0) cc_final: 0.8242 (p0) REVERT: B 58 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7785 (t80) REVERT: B 171 ASP cc_start: 0.8271 (p0) cc_final: 0.7921 (p0) REVERT: B 193 PHE cc_start: 0.8907 (m-80) cc_final: 0.8650 (m-80) REVERT: B 281 ARG cc_start: 0.7508 (ttm110) cc_final: 0.7215 (mtp-110) REVERT: B 609 ASP cc_start: 0.8406 (p0) cc_final: 0.8163 (p0) outliers start: 21 outliers final: 14 residues processed: 97 average time/residue: 0.9856 time to fit residues: 106.3473 Evaluate side-chains 101 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.080948 restraints weight = 15417.119| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.22 r_work: 0.2783 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11642 Z= 0.168 Angle : 0.525 9.799 15852 Z= 0.272 Chirality : 0.040 0.136 1884 Planarity : 0.004 0.045 1934 Dihedral : 5.298 39.637 2136 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.72 % Allowed : 15.08 % Favored : 83.20 % 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: 1.01 (0.23), residues: 1406 helix: 1.59 (0.19), residues: 840 sheet: 3.36 (0.81), residues: 34 loop : -1.02 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 63 HIS 0.003 0.001 HIS A 647 PHE 0.016 0.001 PHE B 130 TYR 0.011 0.001 TYR A 9 ARG 0.011 0.000 ARG A 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3289.39 seconds wall clock time: 59 minutes 20.72 seconds (3560.72 seconds total)