Starting phenix.real_space_refine on Tue Jul 29 14:18:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xuh_33469/07_2025/7xuh_33469.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xuh_33469/07_2025/7xuh_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/cci-nas-00/data/ceres_data/7xuh_33469/07_2025/7xuh_33469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xuh_33469/07_2025/7xuh_33469.map" model { file = "/net/cci-nas-00/data/ceres_data/7xuh_33469/07_2025/7xuh_33469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xuh_33469/07_2025/7xuh_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-5711/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: 6.97, per 1000 atoms: 0.61 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: 2.50 Conformation dependent library (CDL) restraints added in 1.4 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: 1.16 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: 3.54 Time building geometry restraints manager: 3.03 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: 0.05 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 28.050 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.140 ------------------------------------------------------------------------------- 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= 0.502 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 Details of bonding type rmsd hydrogen bonds : bond 0.17912 ( 543) hydrogen bonds : angle 6.33356 ( 1581) covalent geometry : bond 0.01102 (11642) covalent geometry : angle 0.96195 (15852) *********************** 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 to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 1.316 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: 1.3202 time to fit residues: 206.9117 Evaluate side-chains 86 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.081417 restraints weight = 15465.261| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.17 r_work: 0.2791 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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= 0.112 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 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 543) hydrogen bonds : angle 4.28950 ( 1581) covalent geometry : bond 0.00223 (11642) covalent geometry : angle 0.56741 (15852) *********************** 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 to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.213 Fit side-chains REVERT: A 24 ASN cc_start: 0.9101 (m-40) cc_final: 0.8781 (m110) REVERT: A 58 PHE cc_start: 0.8250 (m-80) cc_final: 0.7604 (t80) REVERT: A 171 ASP cc_start: 0.8136 (p0) cc_final: 0.7837 (p0) REVERT: A 193 PHE cc_start: 0.8860 (m-80) cc_final: 0.8640 (m-80) REVERT: A 274 ILE cc_start: 0.8538 (pt) cc_final: 0.8300 (pp) REVERT: B 24 ASN cc_start: 0.9103 (m-40) cc_final: 0.8765 (m110) REVERT: B 58 PHE cc_start: 0.8240 (m-80) cc_final: 0.7662 (t80) REVERT: B 193 PHE cc_start: 0.8834 (m-80) cc_final: 0.8608 (m-80) REVERT: B 274 ILE cc_start: 0.8471 (pt) cc_final: 0.8223 (pp) REVERT: B 285 LYS cc_start: 0.7508 (tmtt) cc_final: 0.7095 (tptt) outliers start: 18 outliers final: 8 residues processed: 110 average time/residue: 0.9037 time to fit residues: 111.3912 Evaluate side-chains 87 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 79 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 119 optimal weight: 0.1980 chunk 139 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.081067 restraints weight = 15737.720| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.20 r_work: 0.2782 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11642 Z= 0.105 Angle : 0.510 5.543 15852 Z= 0.265 Chirality : 0.040 0.125 1884 Planarity : 0.004 0.042 1934 Dihedral : 6.305 59.294 2138 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.80 % Allowed : 11.31 % 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: -0.31 (0.23), residues: 1406 helix: 0.55 (0.19), residues: 830 sheet: 3.36 (0.79), residues: 34 loop : -1.62 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.003 0.001 HIS A 714 PHE 0.018 0.001 PHE A 130 TYR 0.011 0.001 TYR A 9 ARG 0.005 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 543) hydrogen bonds : angle 3.97426 ( 1581) covalent geometry : bond 0.00231 (11642) covalent geometry : angle 0.51031 (15852) *********************** 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 110 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.165 Fit side-chains REVERT: A 24 ASN cc_start: 0.9074 (m-40) cc_final: 0.8735 (m110) REVERT: A 58 PHE cc_start: 0.8221 (m-80) cc_final: 0.7652 (t80) REVERT: A 193 PHE cc_start: 0.8834 (m-80) cc_final: 0.8609 (m-80) REVERT: B 24 ASN cc_start: 0.9075 (m-40) cc_final: 0.8745 (m110) REVERT: B 58 PHE cc_start: 0.8265 (m-80) cc_final: 0.7701 (t80) REVERT: B 171 ASP cc_start: 0.8161 (p0) cc_final: 0.7885 (p0) REVERT: B 193 PHE cc_start: 0.8823 (m-80) cc_final: 0.8596 (m-80) REVERT: B 285 LYS cc_start: 0.7607 (tmtt) cc_final: 0.7232 (tmtm) outliers start: 22 outliers final: 11 residues processed: 102 average time/residue: 0.9750 time to fit residues: 110.1037 Evaluate side-chains 90 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 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 99 ASP 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 684 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 114 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.077113 restraints weight = 15573.932| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.19 r_work: 0.2719 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11642 Z= 0.179 Angle : 0.566 6.851 15852 Z= 0.296 Chirality : 0.043 0.132 1884 Planarity : 0.004 0.051 1934 Dihedral : 6.434 58.750 2136 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.62 % Allowed : 11.80 % Favored : 85.57 % 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: -0.13 (0.23), residues: 1406 helix: 0.69 (0.19), residues: 844 sheet: 3.11 (0.80), residues: 34 loop : -1.57 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.005 0.001 HIS B 647 PHE 0.017 0.001 PHE A 130 TYR 0.021 0.002 TYR A 9 ARG 0.007 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.05371 ( 543) hydrogen bonds : angle 4.00420 ( 1581) covalent geometry : bond 0.00447 (11642) covalent geometry : angle 0.56644 (15852) *********************** 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 118 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 1.319 Fit side-chains REVERT: A 24 ASN cc_start: 0.9032 (m-40) cc_final: 0.8713 (m110) REVERT: A 58 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8004 (t80) REVERT: A 171 ASP cc_start: 0.8236 (p0) cc_final: 0.7868 (p0) REVERT: A 193 PHE cc_start: 0.8946 (m-80) cc_final: 0.8720 (m-80) REVERT: A 281 ARG cc_start: 0.7562 (ttm110) cc_final: 0.6761 (ttm170) REVERT: A 285 LYS cc_start: 0.7661 (tmtt) cc_final: 0.7377 (tmtm) REVERT: B 24 ASN cc_start: 0.9034 (m-40) cc_final: 0.8719 (m110) REVERT: B 58 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7986 (t80) REVERT: B 193 PHE cc_start: 0.8951 (m-80) cc_final: 0.8722 (m-80) REVERT: B 281 ARG cc_start: 0.7563 (ttm110) cc_final: 0.6792 (ttm170) REVERT: B 285 LYS cc_start: 0.7652 (tmtt) cc_final: 0.7358 (tmtm) outliers start: 32 outliers final: 22 residues processed: 109 average time/residue: 1.3952 time to fit residues: 166.6057 Evaluate side-chains 108 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 528 ASP 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 635 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP 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 105 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.112647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.077920 restraints weight = 15519.414| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.20 r_work: 0.2707 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11642 Z= 0.153 Angle : 0.547 7.475 15852 Z= 0.283 Chirality : 0.042 0.129 1884 Planarity : 0.004 0.051 1934 Dihedral : 6.195 56.139 2136 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.30 % Allowed : 12.38 % Favored : 85.33 % 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: 0.87 (0.19), residues: 846 sheet: 2.96 (0.79), residues: 34 loop : -1.42 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 63 HIS 0.004 0.001 HIS A 647 PHE 0.018 0.001 PHE A 130 TYR 0.017 0.001 TYR A 9 ARG 0.006 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04771 ( 543) hydrogen bonds : angle 3.92121 ( 1581) covalent geometry : bond 0.00378 (11642) covalent geometry : angle 0.54699 (15852) *********************** 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 111 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 1.255 Fit side-chains REVERT: A 58 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7933 (t80) REVERT: A 193 PHE cc_start: 0.8904 (m-80) cc_final: 0.8685 (m-80) REVERT: A 281 ARG cc_start: 0.7544 (ttm110) cc_final: 0.6815 (ttm170) REVERT: A 285 LYS cc_start: 0.7684 (tmtt) cc_final: 0.7386 (tmtm) REVERT: A 637 LEU cc_start: 0.7827 (mm) cc_final: 0.7545 (tp) REVERT: B 58 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7908 (t80) REVERT: B 171 ASP cc_start: 0.8318 (p0) cc_final: 0.7988 (p0) REVERT: B 193 PHE cc_start: 0.8898 (m-80) cc_final: 0.8666 (m-80) REVERT: B 281 ARG cc_start: 0.7559 (ttm110) cc_final: 0.6833 (ttm170) REVERT: B 285 LYS cc_start: 0.7719 (tmtt) cc_final: 0.7464 (tmtm) REVERT: B 637 LEU cc_start: 0.7843 (mm) cc_final: 0.7575 (tp) outliers start: 28 outliers final: 20 residues processed: 101 average time/residue: 1.2435 time to fit residues: 138.3553 Evaluate side-chains 101 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 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 635 LEU 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 635 LEU 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 70 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.077532 restraints weight = 15684.801| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.21 r_work: 0.2721 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11642 Z= 0.165 Angle : 0.561 6.612 15852 Z= 0.291 Chirality : 0.042 0.130 1884 Planarity : 0.004 0.051 1934 Dihedral : 6.159 53.782 2136 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.62 % Allowed : 12.54 % Favored : 84.84 % 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: 0.24 (0.23), residues: 1406 helix: 0.97 (0.19), residues: 846 sheet: 2.92 (0.79), residues: 34 loop : -1.37 (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 0.018 0.001 PHE A 130 TYR 0.018 0.001 TYR A 9 ARG 0.005 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 543) hydrogen bonds : angle 3.92152 ( 1581) covalent geometry : bond 0.00410 (11642) covalent geometry : angle 0.56063 (15852) *********************** 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 116 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 2.708 Fit side-chains REVERT: A 58 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7973 (t80) REVERT: A 171 ASP cc_start: 0.8313 (p0) cc_final: 0.7973 (p0) REVERT: A 193 PHE cc_start: 0.8935 (m-80) cc_final: 0.8717 (m-80) REVERT: A 281 ARG cc_start: 0.7621 (ttm110) cc_final: 0.6894 (ttm170) REVERT: A 285 LYS cc_start: 0.7764 (tmtt) cc_final: 0.7515 (tmtm) REVERT: A 637 LEU cc_start: 0.7784 (mm) cc_final: 0.7526 (tp) REVERT: B 58 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7947 (t80) REVERT: B 171 ASP cc_start: 0.8259 (p0) cc_final: 0.7886 (p0) REVERT: B 193 PHE cc_start: 0.8931 (m-80) cc_final: 0.8715 (m-80) REVERT: B 281 ARG cc_start: 0.7587 (ttm110) cc_final: 0.6832 (ttm170) REVERT: B 285 LYS cc_start: 0.7737 (tmtt) cc_final: 0.7488 (tmtm) REVERT: B 637 LEU cc_start: 0.7797 (mm) cc_final: 0.7545 (tp) outliers start: 32 outliers final: 22 residues processed: 106 average time/residue: 1.4903 time to fit residues: 176.6064 Evaluate side-chains 107 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 528 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.079065 restraints weight = 15690.331| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.22 r_work: 0.2748 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11642 Z= 0.126 Angle : 0.527 6.319 15852 Z= 0.274 Chirality : 0.041 0.126 1884 Planarity : 0.004 0.049 1934 Dihedral : 5.859 49.077 2136 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.38 % Allowed : 13.20 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1406 helix: 1.26 (0.19), residues: 832 sheet: 3.02 (0.79), residues: 34 loop : -1.24 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 63 HIS 0.003 0.001 HIS B 647 PHE 0.017 0.001 PHE A 130 TYR 0.013 0.001 TYR A 9 ARG 0.005 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 543) hydrogen bonds : angle 3.83600 ( 1581) covalent geometry : bond 0.00300 (11642) covalent geometry : angle 0.52722 (15852) *********************** 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 116 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 1.244 Fit side-chains REVERT: A 58 PHE cc_start: 0.8247 (m-80) cc_final: 0.7842 (t80) REVERT: A 171 ASP cc_start: 0.8269 (p0) cc_final: 0.7910 (p0) REVERT: A 193 PHE cc_start: 0.8916 (m-80) cc_final: 0.8710 (m-80) REVERT: A 241 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7751 (t) REVERT: A 281 ARG cc_start: 0.7494 (ttm110) cc_final: 0.6825 (ttm170) REVERT: B 58 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7896 (t80) REVERT: B 193 PHE cc_start: 0.8915 (m-80) cc_final: 0.8707 (m-80) REVERT: B 241 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7802 (t) REVERT: B 281 ARG cc_start: 0.7569 (ttm110) cc_final: 0.6877 (ttm170) outliers start: 29 outliers final: 19 residues processed: 106 average time/residue: 1.5997 time to fit residues: 190.4372 Evaluate side-chains 104 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 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 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 514 ILE 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 28 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.079551 restraints weight = 15571.625| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.21 r_work: 0.2753 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11642 Z= 0.121 Angle : 0.521 6.615 15852 Z= 0.273 Chirality : 0.040 0.131 1884 Planarity : 0.004 0.047 1934 Dihedral : 5.692 44.003 2136 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.79 % Allowed : 13.69 % Favored : 83.52 % 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: 0.71 (0.23), residues: 1406 helix: 1.38 (0.19), residues: 836 sheet: 3.10 (0.79), residues: 34 loop : -1.19 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 63 HIS 0.003 0.001 HIS B 647 PHE 0.016 0.001 PHE A 130 TYR 0.013 0.001 TYR A 9 ARG 0.004 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 543) hydrogen bonds : angle 3.77989 ( 1581) covalent geometry : bond 0.00285 (11642) covalent geometry : angle 0.52139 (15852) *********************** 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 117 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 1.314 Fit side-chains REVERT: A 58 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7819 (t80) REVERT: A 241 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7747 (t) REVERT: A 281 ARG cc_start: 0.7563 (ttm110) cc_final: 0.6863 (ttm170) REVERT: B 24 ASN cc_start: 0.8955 (m-40) cc_final: 0.8600 (m110) REVERT: B 58 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7866 (t80) REVERT: B 171 ASP cc_start: 0.8321 (p0) cc_final: 0.7975 (p0) REVERT: B 193 PHE cc_start: 0.8910 (m-80) cc_final: 0.8704 (m-80) REVERT: B 241 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7802 (t) REVERT: B 281 ARG cc_start: 0.7503 (ttm110) cc_final: 0.6816 (ttm170) outliers start: 34 outliers final: 21 residues processed: 104 average time/residue: 0.9478 time to fit residues: 109.9035 Evaluate side-chains 104 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 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 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 514 ILE 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 684 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 111 optimal weight: 0.0870 chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 117 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.082565 restraints weight = 15577.005| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.22 r_work: 0.2806 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2457 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= 0.099 Angle : 0.511 7.352 15852 Z= 0.263 Chirality : 0.040 0.129 1884 Planarity : 0.004 0.043 1934 Dihedral : 5.284 39.237 2136 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.13 % Allowed : 14.34 % Favored : 83.52 % 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: 0.94 (0.23), residues: 1406 helix: 1.53 (0.19), residues: 838 sheet: 3.30 (0.80), residues: 34 loop : -1.04 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 63 HIS 0.002 0.000 HIS A 220 PHE 0.015 0.001 PHE A 130 TYR 0.008 0.001 TYR A 545 ARG 0.004 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 543) hydrogen bonds : angle 3.67728 ( 1581) covalent geometry : bond 0.00217 (11642) covalent geometry : angle 0.51114 (15852) *********************** 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 121 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 1.335 Fit side-chains REVERT: A 24 ASN cc_start: 0.8942 (m-40) cc_final: 0.8579 (m110) REVERT: A 58 PHE cc_start: 0.8117 (m-80) cc_final: 0.7725 (t80) REVERT: A 171 ASP cc_start: 0.8269 (p0) cc_final: 0.7925 (p0) REVERT: A 241 VAL cc_start: 0.7832 (OUTLIER) cc_final: 0.7568 (t) REVERT: A 281 ARG cc_start: 0.7530 (ttm110) cc_final: 0.6850 (ttm170) REVERT: A 558 ASP cc_start: 0.8429 (t0) cc_final: 0.8112 (m-30) REVERT: B 24 ASN cc_start: 0.8947 (m-40) cc_final: 0.8567 (m110) REVERT: B 58 PHE cc_start: 0.8101 (m-80) cc_final: 0.7665 (t80) REVERT: B 171 ASP cc_start: 0.8242 (p0) cc_final: 0.7890 (p0) REVERT: B 241 VAL cc_start: 0.7832 (OUTLIER) cc_final: 0.7566 (t) REVERT: B 281 ARG cc_start: 0.7488 (ttm110) cc_final: 0.6801 (ttm170) outliers start: 26 outliers final: 14 residues processed: 111 average time/residue: 0.9625 time to fit residues: 119.2902 Evaluate side-chains 105 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 241 VAL 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 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 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 27 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 126 optimal weight: 0.0270 chunk 101 optimal weight: 0.0000 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 548 ASN B 322 ASN B 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.082148 restraints weight = 15061.134| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.19 r_work: 0.2773 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11642 Z= 0.095 Angle : 0.503 10.087 15852 Z= 0.256 Chirality : 0.040 0.197 1884 Planarity : 0.004 0.038 1934 Dihedral : 5.086 39.041 2136 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.48 % Allowed : 15.00 % Favored : 83.52 % 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: 1.14 (0.24), residues: 1406 helix: 1.68 (0.19), residues: 838 sheet: 3.40 (0.79), residues: 34 loop : -0.94 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 63 HIS 0.003 0.001 HIS B 38 PHE 0.015 0.001 PHE A 130 TYR 0.008 0.001 TYR A 545 ARG 0.003 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 543) hydrogen bonds : angle 3.62946 ( 1581) covalent geometry : bond 0.00205 (11642) covalent geometry : angle 0.50287 (15852) ********************** 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 117 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.260 Fit side-chains REVERT: A 24 ASN cc_start: 0.8990 (m-40) cc_final: 0.8649 (m110) REVERT: A 58 PHE cc_start: 0.8110 (m-80) cc_final: 0.7769 (t80) REVERT: A 171 ASP cc_start: 0.8312 (p0) cc_final: 0.7963 (p0) REVERT: A 241 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7595 (t) REVERT: A 281 ARG cc_start: 0.7534 (ttm110) cc_final: 0.6799 (ttm170) REVERT: A 558 ASP cc_start: 0.8505 (t0) cc_final: 0.8223 (m-30) REVERT: B 24 ASN cc_start: 0.8972 (m-40) cc_final: 0.8646 (m110) REVERT: B 58 PHE cc_start: 0.8102 (m-80) cc_final: 0.7701 (t80) REVERT: B 171 ASP cc_start: 0.8316 (p0) cc_final: 0.7982 (p0) REVERT: B 241 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7605 (t) REVERT: B 281 ARG cc_start: 0.7579 (ttm110) cc_final: 0.6892 (ttm170) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.8702 time to fit residues: 107.3520 Evaluate side-chains 107 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 241 VAL 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 B residue 99 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 241 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 108 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 56 optimal weight: 0.0670 chunk 105 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 overall best weight: 2.0122 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.078298 restraints weight = 15574.084| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.22 r_work: 0.2713 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11642 Z= 0.171 Angle : 0.579 9.653 15852 Z= 0.298 Chirality : 0.042 0.140 1884 Planarity : 0.004 0.045 1934 Dihedral : 5.547 43.342 2136 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.31 % Allowed : 15.98 % Favored : 82.70 % 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: 1406 helix: 1.42 (0.19), residues: 848 sheet: 3.06 (0.78), residues: 34 loop : -1.09 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.004 0.001 HIS A 647 PHE 0.017 0.001 PHE B 130 TYR 0.017 0.002 TYR A 9 ARG 0.003 0.000 ARG B 281 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 543) hydrogen bonds : angle 3.79294 ( 1581) covalent geometry : bond 0.00424 (11642) covalent geometry : angle 0.57931 (15852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8736.00 seconds wall clock time: 156 minutes 41.22 seconds (9401.22 seconds total)