Starting phenix.real_space_refine on Sat Sep 12 22:56:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wkn_21705/09_2026/6wkn_21705.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wkn_21705/09_2026/6wkn_21705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wkn_21705/09_2026/6wkn_21705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wkn_21705/09_2026/6wkn_21705.map" model { file = "/net/cci-nas-00/data/ceres_data/6wkn_21705/09_2026/6wkn_21705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wkn_21705/09_2026/6wkn_21705.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6wkn_21705/09_2026/6wkn_21705.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wkn_21705/09_2026/6wkn_21705.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12636 2.51 5 N 3240 2.21 5 O 3332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19320 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 11, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'LQ4': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 5.26, per 1000 atoms: 0.27 Number of scatterers: 19320 At special positions: 0 Unit cell: (138.27, 138.27, 113.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3332 8.00 N 3240 7.00 C 12636 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: 1.90 Conformation dependent library (CDL) restraints added in 922.8 milliseconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 60.9% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 145 removed outlier: 3.920A pdb=" N LEU A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.643A pdb=" N ALA A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.610A pdb=" N PHE A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.579A pdb=" N MET A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 375 through 413 removed outlier: 3.961A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.716A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.928A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.709A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 559 removed outlier: 5.517A pdb=" N ARG A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASP A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 619 through 650 Processing helix chain 'A' and resid 652 through 673 removed outlier: 3.584A pdb=" N SER A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 145 removed outlier: 3.921A pdb=" N LEU B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.643A pdb=" N ALA B 265 " --> pdb=" O PRO B 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.610A pdb=" N PHE B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.580A pdb=" N MET B 372 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 375 through 413 removed outlier: 3.961A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 470 through 492 removed outlier: 3.717A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.928A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.709A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 559 removed outlier: 5.516A pdb=" N ARG B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASP B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 619 through 650 Processing helix chain 'B' and resid 652 through 673 removed outlier: 3.584A pdb=" N SER B 656 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 145 removed outlier: 3.920A pdb=" N LEU C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 140 " --> pdb=" O ILE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.643A pdb=" N ALA C 265 " --> pdb=" O PRO C 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.610A pdb=" N PHE C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.580A pdb=" N MET C 372 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 375 through 413 removed outlier: 3.962A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 381 " --> pdb=" O PRO C 377 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 470 through 492 removed outlier: 3.716A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.928A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 517 removed outlier: 3.709A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 559 removed outlier: 5.517A pdb=" N ARG C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASP C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 619 through 650 Processing helix chain 'C' and resid 652 through 673 removed outlier: 3.584A pdb=" N SER C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 145 removed outlier: 3.920A pdb=" N LEU D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 140 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.643A pdb=" N ALA D 265 " --> pdb=" O PRO D 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.610A pdb=" N PHE D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.578A pdb=" N MET D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 375 through 413 removed outlier: 3.960A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 381 " --> pdb=" O PRO D 377 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 470 through 492 removed outlier: 3.716A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 3.928A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 517 removed outlier: 3.709A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 559 removed outlier: 5.516A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASP D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 619 through 650 Processing helix chain 'D' and resid 652 through 673 removed outlier: 3.584A pdb=" N SER D 656 " --> pdb=" O VAL D 652 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.953A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP A 700 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 687 " --> pdb=" O CYS A 704 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.952A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP B 700 " --> pdb=" O VAL B 691 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 687 " --> pdb=" O CYS B 704 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.953A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP C 700 " --> pdb=" O VAL C 691 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG C 687 " --> pdb=" O CYS C 704 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.953A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP D 700 " --> pdb=" O VAL D 691 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 687 " --> pdb=" O CYS D 704 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3204 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: 3.08 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2984 1.31 - 1.43: 5552 1.43 - 1.56: 11080 1.56 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 19788 Sorted by residual: bond pdb=" C13 LQ4 C 801 " pdb=" C14 LQ4 C 801 " ideal model delta sigma weight residual 1.332 1.500 -0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C13 LQ4 A 801 " pdb=" C14 LQ4 A 801 " ideal model delta sigma weight residual 1.332 1.500 -0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C13 LQ4 D 801 " pdb=" C14 LQ4 D 801 " ideal model delta sigma weight residual 1.332 1.500 -0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C13 LQ4 B 801 " pdb=" C14 LQ4 B 801 " ideal model delta sigma weight residual 1.332 1.499 -0.167 2.00e-02 2.50e+03 7.00e+01 bond pdb=" C15 LQ4 B 801 " pdb=" N10 LQ4 B 801 " ideal model delta sigma weight residual 1.390 1.481 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 19783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 26045 1.79 - 3.58: 679 3.58 - 5.37: 100 5.37 - 7.15: 36 7.15 - 8.94: 8 Bond angle restraints: 26868 Sorted by residual: angle pdb=" C GLY D 204 " pdb=" N THR D 205 " pdb=" CA THR D 205 " ideal model delta sigma weight residual 122.46 127.64 -5.18 1.41e+00 5.03e-01 1.35e+01 angle pdb=" C GLY A 204 " pdb=" N THR A 205 " pdb=" CA THR A 205 " ideal model delta sigma weight residual 122.46 127.64 -5.18 1.41e+00 5.03e-01 1.35e+01 angle pdb=" C GLY B 204 " pdb=" N THR B 205 " pdb=" CA THR B 205 " ideal model delta sigma weight residual 122.46 127.64 -5.18 1.41e+00 5.03e-01 1.35e+01 angle pdb=" C GLY C 204 " pdb=" N THR C 205 " pdb=" CA THR C 205 " ideal model delta sigma weight residual 122.46 127.62 -5.16 1.41e+00 5.03e-01 1.34e+01 angle pdb=" C PHE A 467 " pdb=" N MET A 468 " pdb=" CA MET A 468 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+01 ... (remaining 26863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 10277 16.51 - 33.02: 907 33.02 - 49.54: 276 49.54 - 66.05: 88 66.05 - 82.56: 40 Dihedral angle restraints: 11588 sinusoidal: 4508 harmonic: 7080 Sorted by residual: dihedral pdb=" CA VAL B 532 " pdb=" C VAL B 532 " pdb=" N ILE B 533 " pdb=" CA ILE B 533 " ideal model delta harmonic sigma weight residual -180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA VAL C 532 " pdb=" C VAL C 532 " pdb=" N ILE C 533 " pdb=" CA ILE C 533 " ideal model delta harmonic sigma weight residual -180.00 -158.51 -21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA VAL A 532 " pdb=" C VAL A 532 " pdb=" N ILE A 533 " pdb=" CA ILE A 533 " ideal model delta harmonic sigma weight residual -180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 11585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1820 0.033 - 0.065: 861 0.065 - 0.097: 273 0.097 - 0.130: 94 0.130 - 0.162: 12 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CA THR D 205 " pdb=" N THR D 205 " pdb=" C THR D 205 " pdb=" CB THR D 205 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA THR C 205 " pdb=" N THR C 205 " pdb=" C THR C 205 " pdb=" CB THR C 205 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA THR B 205 " pdb=" N THR B 205 " pdb=" C THR B 205 " pdb=" CB THR B 205 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 3057 not shown) Planarity restraints: 3324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 LQ4 B 801 " -0.053 2.00e-02 2.50e+03 2.77e-01 1.53e+03 pdb=" C08 LQ4 B 801 " -0.076 2.00e-02 2.50e+03 pdb=" C11 LQ4 B 801 " 0.273 2.00e-02 2.50e+03 pdb=" C14 LQ4 B 801 " -0.510 2.00e-02 2.50e+03 pdb=" C15 LQ4 B 801 " 0.052 2.00e-02 2.50e+03 pdb=" N10 LQ4 B 801 " 0.091 2.00e-02 2.50e+03 pdb=" O09 LQ4 B 801 " -0.230 2.00e-02 2.50e+03 pdb=" O16 LQ4 B 801 " 0.453 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 LQ4 D 801 " -0.053 2.00e-02 2.50e+03 2.77e-01 1.53e+03 pdb=" C08 LQ4 D 801 " -0.076 2.00e-02 2.50e+03 pdb=" C11 LQ4 D 801 " 0.273 2.00e-02 2.50e+03 pdb=" C14 LQ4 D 801 " -0.510 2.00e-02 2.50e+03 pdb=" C15 LQ4 D 801 " 0.052 2.00e-02 2.50e+03 pdb=" N10 LQ4 D 801 " 0.091 2.00e-02 2.50e+03 pdb=" O09 LQ4 D 801 " -0.230 2.00e-02 2.50e+03 pdb=" O16 LQ4 D 801 " 0.454 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 LQ4 A 801 " -0.053 2.00e-02 2.50e+03 2.77e-01 1.53e+03 pdb=" C08 LQ4 A 801 " -0.076 2.00e-02 2.50e+03 pdb=" C11 LQ4 A 801 " 0.273 2.00e-02 2.50e+03 pdb=" C14 LQ4 A 801 " -0.510 2.00e-02 2.50e+03 pdb=" C15 LQ4 A 801 " 0.052 2.00e-02 2.50e+03 pdb=" N10 LQ4 A 801 " 0.091 2.00e-02 2.50e+03 pdb=" O09 LQ4 A 801 " -0.230 2.00e-02 2.50e+03 pdb=" O16 LQ4 A 801 " 0.454 2.00e-02 2.50e+03 ... (remaining 3321 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4850 2.79 - 3.32: 17337 3.32 - 3.85: 32641 3.85 - 4.37: 37410 4.37 - 4.90: 65750 Nonbonded interactions: 157988 Sorted by model distance: nonbonded pdb=" OH TYR A 271 " pdb=" OE1 GLU A 288 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR D 271 " pdb=" OE1 GLU D 288 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR C 271 " pdb=" OE1 GLU C 288 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR B 271 " pdb=" OE1 GLU B 288 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR A 544 " pdb=" OG1 THR A 604 " model vdw 2.276 3.040 ... (remaining 157983 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.390 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.007 0.168 19788 Z= 0.295 Angle : 0.738 8.943 26868 Z= 0.392 Chirality : 0.043 0.162 3060 Planarity : 0.011 0.277 3324 Dihedral : 15.699 82.559 7012 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.53 % Allowed : 11.37 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.14), residues: 2384 helix: -1.53 (0.11), residues: 1400 sheet: -1.05 (0.61), residues: 84 loop : -2.54 (0.16), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 392 TYR 0.017 0.002 TYR B 343 PHE 0.023 0.002 PHE B 311 TRP 0.016 0.002 TRP B 677 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.29 (19788) covalent geometry : angle 0.73817 / 0.39 (26868) hydrogen bonds : bond 0.14391 / 9.97 ( 1080) hydrogen bonds : angle 6.30728 / 4.34 ( 3204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 448 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8800 (tp) cc_final: 0.8496 (mt) REVERT: A 243 ASP cc_start: 0.8515 (p0) cc_final: 0.8035 (p0) REVERT: A 269 HIS cc_start: 0.6808 (m90) cc_final: 0.6552 (m90) REVERT: A 277 MET cc_start: 0.8038 (ttm) cc_final: 0.7732 (ttp) REVERT: A 453 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8482 (mt) REVERT: A 468 MET cc_start: 0.6470 (mtp) cc_final: 0.6211 (mtm) REVERT: A 474 ILE cc_start: 0.8552 (pt) cc_final: 0.8236 (mt) REVERT: A 599 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: A 631 LEU cc_start: 0.8740 (tt) cc_final: 0.8489 (tt) REVERT: A 638 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.7954 (mp) REVERT: A 685 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: B 183 LEU cc_start: 0.8821 (tp) cc_final: 0.8514 (mt) REVERT: B 243 ASP cc_start: 0.8513 (p0) cc_final: 0.8024 (p0) REVERT: B 269 HIS cc_start: 0.6772 (m90) cc_final: 0.6527 (m90) REVERT: B 277 MET cc_start: 0.8017 (ttm) cc_final: 0.7710 (ttp) REVERT: B 453 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8495 (mt) REVERT: B 474 ILE cc_start: 0.8564 (pt) cc_final: 0.8293 (mt) REVERT: B 599 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7750 (tp30) REVERT: B 631 LEU cc_start: 0.8745 (tt) cc_final: 0.8491 (tt) REVERT: B 638 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.7921 (mp) REVERT: B 685 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: C 183 LEU cc_start: 0.8798 (tp) cc_final: 0.8486 (mt) REVERT: C 243 ASP cc_start: 0.8524 (p0) cc_final: 0.8041 (p0) REVERT: C 269 HIS cc_start: 0.6774 (m90) cc_final: 0.6519 (m90) REVERT: C 277 MET cc_start: 0.8035 (ttm) cc_final: 0.7721 (ttp) REVERT: C 453 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8478 (mt) REVERT: C 468 MET cc_start: 0.6465 (mtp) cc_final: 0.6199 (mtm) REVERT: C 474 ILE cc_start: 0.8579 (pt) cc_final: 0.8299 (mt) REVERT: C 599 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7777 (tp30) REVERT: C 631 LEU cc_start: 0.8746 (tt) cc_final: 0.8492 (tt) REVERT: C 638 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.7980 (mp) REVERT: C 685 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: D 183 LEU cc_start: 0.8783 (tp) cc_final: 0.8477 (mt) REVERT: D 243 ASP cc_start: 0.8535 (p0) cc_final: 0.8044 (p0) REVERT: D 269 HIS cc_start: 0.6785 (m90) cc_final: 0.6528 (m90) REVERT: D 277 MET cc_start: 0.8032 (ttm) cc_final: 0.7727 (ttp) REVERT: D 453 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8474 (mt) REVERT: D 474 ILE cc_start: 0.8577 (pt) cc_final: 0.8309 (mt) REVERT: D 599 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7800 (tp30) REVERT: D 631 LEU cc_start: 0.8752 (tt) cc_final: 0.8494 (tt) REVERT: D 638 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.7927 (mp) REVERT: D 685 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6683 (mp0) outliers start: 92 outliers final: 33 residues processed: 524 average time/residue: 0.1434 time to fit residues: 114.7902 Evaluate side-chains 337 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 288 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 599 GLU Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 685 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 530 GLN ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 GLN ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN D 530 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.157637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137122 restraints weight = 25060.606| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.55 r_work: 0.3524 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19788 Z= 0.142 Angle : 0.543 6.740 26868 Z= 0.282 Chirality : 0.038 0.124 3060 Planarity : 0.005 0.046 3324 Dihedral : 9.123 89.258 2754 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.28 % Allowed : 15.31 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2384 helix: 0.40 (0.13), residues: 1424 sheet: -1.57 (0.49), residues: 112 loop : -1.97 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 619 TYR 0.015 0.001 TYR D 98 PHE 0.016 0.001 PHE D 311 TRP 0.012 0.001 TRP D 677 HIS 0.002 0.001 HIS D 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (19788) covalent geometry : angle 0.54318 / 0.28 (26868) hydrogen bonds : bond 0.04059 / 2.68 ( 1080) hydrogen bonds : angle 4.04316 / 2.76 ( 3204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 306 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8766 (tp) cc_final: 0.8512 (mt) REVERT: A 243 ASP cc_start: 0.8461 (p0) cc_final: 0.7901 (p0) REVERT: A 269 HIS cc_start: 0.7467 (m90) cc_final: 0.7201 (m90) REVERT: A 277 MET cc_start: 0.8515 (ttm) cc_final: 0.8301 (ttp) REVERT: A 368 ASN cc_start: 0.8255 (p0) cc_final: 0.7972 (p0) REVERT: A 412 TYR cc_start: 0.7584 (t80) cc_final: 0.7368 (t80) REVERT: A 631 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 634 TYR cc_start: 0.8420 (t80) cc_final: 0.8193 (t80) REVERT: A 638 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8124 (mp) REVERT: A 645 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7240 (mtm) REVERT: A 677 TRP cc_start: 0.8026 (OUTLIER) cc_final: 0.7015 (p-90) REVERT: A 685 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7919 (mm-30) REVERT: B 183 LEU cc_start: 0.8763 (tp) cc_final: 0.8514 (mt) REVERT: B 243 ASP cc_start: 0.8434 (p0) cc_final: 0.7896 (p0) REVERT: B 269 HIS cc_start: 0.7487 (m90) cc_final: 0.7211 (m90) REVERT: B 277 MET cc_start: 0.8494 (ttm) cc_final: 0.8277 (ttp) REVERT: B 368 ASN cc_start: 0.8272 (p0) cc_final: 0.7987 (p0) REVERT: B 412 TYR cc_start: 0.7581 (t80) cc_final: 0.7355 (t80) REVERT: B 631 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8290 (mp) REVERT: B 634 TYR cc_start: 0.8423 (t80) cc_final: 0.8195 (t80) REVERT: B 638 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8089 (mp) REVERT: B 645 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7243 (mtm) REVERT: B 677 TRP cc_start: 0.8023 (OUTLIER) cc_final: 0.6933 (p-90) REVERT: B 685 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7961 (mm-30) REVERT: C 183 LEU cc_start: 0.8780 (tp) cc_final: 0.8521 (mt) REVERT: C 243 ASP cc_start: 0.8469 (p0) cc_final: 0.7920 (p0) REVERT: C 269 HIS cc_start: 0.7467 (m90) cc_final: 0.7203 (m90) REVERT: C 277 MET cc_start: 0.8486 (ttm) cc_final: 0.8257 (ttp) REVERT: C 368 ASN cc_start: 0.8234 (p0) cc_final: 0.7956 (p0) REVERT: C 412 TYR cc_start: 0.7599 (t80) cc_final: 0.7379 (t80) REVERT: C 631 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8289 (mp) REVERT: C 634 TYR cc_start: 0.8418 (t80) cc_final: 0.8191 (t80) REVERT: C 638 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8124 (mp) REVERT: C 645 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7267 (mtm) REVERT: C 677 TRP cc_start: 0.8017 (OUTLIER) cc_final: 0.6930 (p-90) REVERT: C 685 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: D 183 LEU cc_start: 0.8757 (tp) cc_final: 0.8505 (mt) REVERT: D 243 ASP cc_start: 0.8447 (p0) cc_final: 0.7896 (p0) REVERT: D 269 HIS cc_start: 0.7473 (m90) cc_final: 0.7206 (m90) REVERT: D 277 MET cc_start: 0.8518 (ttm) cc_final: 0.8293 (ttp) REVERT: D 368 ASN cc_start: 0.8258 (p0) cc_final: 0.7972 (p0) REVERT: D 412 TYR cc_start: 0.7588 (t80) cc_final: 0.7353 (t80) REVERT: D 631 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8300 (mp) REVERT: D 634 TYR cc_start: 0.8445 (t80) cc_final: 0.8215 (t80) REVERT: D 638 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8104 (mp) REVERT: D 645 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7263 (mtm) REVERT: D 677 TRP cc_start: 0.8025 (OUTLIER) cc_final: 0.6941 (p-90) REVERT: D 685 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7961 (mm-30) outliers start: 87 outliers final: 56 residues processed: 363 average time/residue: 0.1263 time to fit residues: 73.7057 Evaluate side-chains 331 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 255 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 677 TRP Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 214 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN B 294 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 294 GLN ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN D 294 GLN ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.152935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132571 restraints weight = 25238.541| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.54 r_work: 0.3460 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19788 Z= 0.229 Angle : 0.628 7.800 26868 Z= 0.320 Chirality : 0.041 0.145 3060 Planarity : 0.005 0.053 3324 Dihedral : 8.438 84.955 2716 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.66 % Allowed : 14.86 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2384 helix: 0.74 (0.13), residues: 1452 sheet: -1.39 (0.50), residues: 112 loop : -1.75 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 458 TYR 0.020 0.002 TYR B 343 PHE 0.019 0.002 PHE A 311 TRP 0.016 0.001 TRP A 677 HIS 0.006 0.001 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (19788) covalent geometry : angle 0.62840 / 0.32 (26868) hydrogen bonds : bond 0.04554 / 3.00 ( 1080) hydrogen bonds : angle 4.04797 / 2.77 ( 3204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 290 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.8760 (p0) cc_final: 0.8331 (p0) REVERT: A 269 HIS cc_start: 0.7654 (m90) cc_final: 0.7349 (m90) REVERT: A 277 MET cc_start: 0.8642 (ttm) cc_final: 0.8374 (ttp) REVERT: A 412 TYR cc_start: 0.7627 (t80) cc_final: 0.7336 (t80) REVERT: A 631 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 638 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8077 (mp) REVERT: A 645 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7351 (mtm) REVERT: A 677 TRP cc_start: 0.8114 (OUTLIER) cc_final: 0.7445 (p-90) REVERT: A 685 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: B 243 ASP cc_start: 0.8729 (p0) cc_final: 0.8301 (p0) REVERT: B 269 HIS cc_start: 0.7634 (m90) cc_final: 0.7349 (m90) REVERT: B 277 MET cc_start: 0.8638 (ttm) cc_final: 0.8371 (ttp) REVERT: B 412 TYR cc_start: 0.7643 (t80) cc_final: 0.7354 (t80) REVERT: B 533 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7237 (tt) REVERT: B 631 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8296 (mp) REVERT: B 638 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8196 (mp) REVERT: B 645 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7349 (mtm) REVERT: B 677 TRP cc_start: 0.8115 (OUTLIER) cc_final: 0.7376 (p-90) REVERT: B 685 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: C 243 ASP cc_start: 0.8748 (p0) cc_final: 0.8322 (p0) REVERT: C 269 HIS cc_start: 0.7632 (m90) cc_final: 0.7348 (m90) REVERT: C 277 MET cc_start: 0.8618 (ttm) cc_final: 0.8352 (ttp) REVERT: C 412 TYR cc_start: 0.7630 (t80) cc_final: 0.7354 (t80) REVERT: C 631 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8301 (mp) REVERT: C 638 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8085 (mp) REVERT: C 645 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7379 (mtm) REVERT: C 677 TRP cc_start: 0.8115 (OUTLIER) cc_final: 0.7372 (p-90) REVERT: C 685 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: D 243 ASP cc_start: 0.8729 (p0) cc_final: 0.8301 (p0) REVERT: D 269 HIS cc_start: 0.7639 (m90) cc_final: 0.7356 (m90) REVERT: D 277 MET cc_start: 0.8639 (ttm) cc_final: 0.8371 (ttp) REVERT: D 412 TYR cc_start: 0.7605 (t80) cc_final: 0.7309 (t80) REVERT: D 533 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7213 (tt) REVERT: D 631 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8307 (mp) REVERT: D 638 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8198 (mp) REVERT: D 645 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7364 (mtm) REVERT: D 677 TRP cc_start: 0.8131 (OUTLIER) cc_final: 0.7391 (p-90) REVERT: D 685 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7659 (mp0) outliers start: 115 outliers final: 66 residues processed: 359 average time/residue: 0.1254 time to fit residues: 72.5327 Evaluate side-chains 346 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 258 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 677 TRP Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 202 optimal weight: 0.4980 chunk 174 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN B 530 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN D 530 GLN ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.157262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137700 restraints weight = 24902.066| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.44 r_work: 0.3521 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19788 Z= 0.123 Angle : 0.512 6.250 26868 Z= 0.263 Chirality : 0.037 0.118 3060 Planarity : 0.004 0.045 3324 Dihedral : 8.333 88.095 2716 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.64 % Allowed : 18.01 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.17), residues: 2384 helix: 1.56 (0.14), residues: 1404 sheet: -1.16 (0.51), residues: 112 loop : -1.49 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 684 TYR 0.016 0.001 TYR C 98 PHE 0.013 0.001 PHE A 311 TRP 0.012 0.001 TRP C 677 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (19788) covalent geometry : angle 0.51165 / 0.26 (26868) hydrogen bonds : bond 0.03587 / 2.36 ( 1080) hydrogen bonds : angle 3.76149 / 2.56 ( 3204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 290 time to evaluate : 0.702 Fit side-chains REVERT: A 75 PHE cc_start: 0.5591 (OUTLIER) cc_final: 0.5124 (t80) REVERT: A 243 ASP cc_start: 0.8582 (p0) cc_final: 0.8171 (p0) REVERT: A 269 HIS cc_start: 0.7522 (m90) cc_final: 0.7239 (m90) REVERT: A 277 MET cc_start: 0.8562 (ttm) cc_final: 0.8301 (ttp) REVERT: A 412 TYR cc_start: 0.7547 (t80) cc_final: 0.7245 (t80) REVERT: A 631 LEU cc_start: 0.8697 (tt) cc_final: 0.8296 (mp) REVERT: A 638 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8058 (mp) REVERT: A 645 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7360 (mtm) REVERT: A 677 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7085 (p-90) REVERT: B 75 PHE cc_start: 0.5574 (OUTLIER) cc_final: 0.5093 (t80) REVERT: B 243 ASP cc_start: 0.8545 (p0) cc_final: 0.8132 (p0) REVERT: B 269 HIS cc_start: 0.7516 (m90) cc_final: 0.7238 (m90) REVERT: B 277 MET cc_start: 0.8509 (ttm) cc_final: 0.8259 (ttp) REVERT: B 533 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7222 (tt) REVERT: B 631 LEU cc_start: 0.8679 (tt) cc_final: 0.8265 (mp) REVERT: B 645 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7335 (mtm) REVERT: B 677 TRP cc_start: 0.8078 (OUTLIER) cc_final: 0.7106 (p-90) REVERT: C 75 PHE cc_start: 0.5609 (OUTLIER) cc_final: 0.5132 (t80) REVERT: C 243 ASP cc_start: 0.8581 (p0) cc_final: 0.8163 (p0) REVERT: C 269 HIS cc_start: 0.7567 (m90) cc_final: 0.7282 (m90) REVERT: C 277 MET cc_start: 0.8519 (ttm) cc_final: 0.8264 (ttp) REVERT: C 412 TYR cc_start: 0.7568 (t80) cc_final: 0.7219 (t80) REVERT: C 631 LEU cc_start: 0.8692 (tt) cc_final: 0.8286 (mp) REVERT: C 638 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8089 (mp) REVERT: C 645 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7377 (mtm) REVERT: C 677 TRP cc_start: 0.8071 (OUTLIER) cc_final: 0.7081 (p-90) REVERT: D 75 PHE cc_start: 0.5585 (OUTLIER) cc_final: 0.5120 (t80) REVERT: D 243 ASP cc_start: 0.8563 (p0) cc_final: 0.8140 (p0) REVERT: D 269 HIS cc_start: 0.7537 (m90) cc_final: 0.7255 (m90) REVERT: D 277 MET cc_start: 0.8544 (ttm) cc_final: 0.8280 (ttp) REVERT: D 533 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7197 (tt) REVERT: D 631 LEU cc_start: 0.8690 (tt) cc_final: 0.8280 (mp) REVERT: D 645 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7337 (mtm) REVERT: D 677 TRP cc_start: 0.8087 (OUTLIER) cc_final: 0.7091 (p-90) outliers start: 74 outliers final: 48 residues processed: 347 average time/residue: 0.1328 time to fit residues: 73.1417 Evaluate side-chains 330 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 266 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 677 TRP Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 171 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 238 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.156224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136142 restraints weight = 24951.076| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.46 r_work: 0.3509 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19788 Z= 0.142 Angle : 0.533 6.670 26868 Z= 0.271 Chirality : 0.037 0.147 3060 Planarity : 0.004 0.045 3324 Dihedral : 7.973 87.992 2691 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.23 % Allowed : 17.96 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2384 helix: 1.82 (0.14), residues: 1396 sheet: -0.88 (0.53), residues: 112 loop : -1.46 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 684 TYR 0.013 0.001 TYR C 98 PHE 0.014 0.001 PHE B 311 TRP 0.013 0.001 TRP D 677 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (19788) covalent geometry : angle 0.53331 / 0.27 (26868) hydrogen bonds : bond 0.03714 / 2.45 ( 1080) hydrogen bonds : angle 3.74666 / 2.55 ( 3204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 282 time to evaluate : 0.730 Fit side-chains REVERT: A 75 PHE cc_start: 0.5556 (OUTLIER) cc_final: 0.5197 (t80) REVERT: A 243 ASP cc_start: 0.8600 (p0) cc_final: 0.8021 (p0) REVERT: A 269 HIS cc_start: 0.7514 (m90) cc_final: 0.7236 (m90) REVERT: A 277 MET cc_start: 0.8589 (ttm) cc_final: 0.8279 (ttp) REVERT: A 631 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8300 (mp) REVERT: A 645 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7323 (mtm) REVERT: A 677 TRP cc_start: 0.8084 (OUTLIER) cc_final: 0.7097 (p-90) REVERT: A 685 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: B 75 PHE cc_start: 0.5538 (OUTLIER) cc_final: 0.5167 (t80) REVERT: B 243 ASP cc_start: 0.8567 (p0) cc_final: 0.8109 (p0) REVERT: B 269 HIS cc_start: 0.7517 (m90) cc_final: 0.7241 (m90) REVERT: B 277 MET cc_start: 0.8549 (ttm) cc_final: 0.8336 (ttp) REVERT: B 533 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.7195 (tt) REVERT: B 631 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8260 (mp) REVERT: B 645 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7296 (mtm) REVERT: B 677 TRP cc_start: 0.8097 (OUTLIER) cc_final: 0.7138 (p-90) REVERT: B 685 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: C 75 PHE cc_start: 0.5544 (OUTLIER) cc_final: 0.5175 (t80) REVERT: C 243 ASP cc_start: 0.8594 (p0) cc_final: 0.8134 (p0) REVERT: C 269 HIS cc_start: 0.7554 (m90) cc_final: 0.7273 (m90) REVERT: C 277 MET cc_start: 0.8572 (ttm) cc_final: 0.8264 (ttp) REVERT: C 631 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8287 (mp) REVERT: C 645 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7324 (mtm) REVERT: C 677 TRP cc_start: 0.8074 (OUTLIER) cc_final: 0.7116 (p-90) REVERT: C 685 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: D 75 PHE cc_start: 0.5547 (OUTLIER) cc_final: 0.5185 (t80) REVERT: D 243 ASP cc_start: 0.8581 (p0) cc_final: 0.8118 (p0) REVERT: D 269 HIS cc_start: 0.7538 (m90) cc_final: 0.7254 (m90) REVERT: D 277 MET cc_start: 0.8573 (ttm) cc_final: 0.8259 (ttp) REVERT: D 631 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8278 (mp) REVERT: D 645 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7315 (mtm) REVERT: D 677 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.7130 (p-90) REVERT: D 685 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7434 (mp0) outliers start: 86 outliers final: 61 residues processed: 339 average time/residue: 0.1172 time to fit residues: 64.8891 Evaluate side-chains 349 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 267 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 677 TRP Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 67 optimal weight: 6.9990 chunk 222 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.158350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138637 restraints weight = 24716.999| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.39 r_work: 0.3541 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19788 Z= 0.112 Angle : 0.504 8.222 26868 Z= 0.255 Chirality : 0.036 0.146 3060 Planarity : 0.004 0.050 3324 Dihedral : 7.836 89.960 2687 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.13 % Allowed : 18.90 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2384 helix: 2.06 (0.14), residues: 1396 sheet: -0.62 (0.54), residues: 112 loop : -1.33 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 193 TYR 0.012 0.001 TYR B 98 PHE 0.012 0.001 PHE A 311 TRP 0.011 0.001 TRP A 677 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (19788) covalent geometry : angle 0.50397 / 0.25 (26868) hydrogen bonds : bond 0.03421 / 2.25 ( 1080) hydrogen bonds : angle 3.65902 / 2.50 ( 3204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 286 time to evaluate : 0.741 Fit side-chains REVERT: A 75 PHE cc_start: 0.5553 (OUTLIER) cc_final: 0.5190 (t80) REVERT: A 243 ASP cc_start: 0.8545 (p0) cc_final: 0.8117 (p0) REVERT: A 277 MET cc_start: 0.8618 (ttm) cc_final: 0.8380 (tpp) REVERT: A 280 ARG cc_start: 0.7749 (ptp90) cc_final: 0.6982 (ptm160) REVERT: A 631 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8261 (mp) REVERT: A 645 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7305 (mtt) REVERT: A 677 TRP cc_start: 0.8087 (OUTLIER) cc_final: 0.7101 (p-90) REVERT: A 685 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: B 75 PHE cc_start: 0.5498 (OUTLIER) cc_final: 0.5183 (t80) REVERT: B 243 ASP cc_start: 0.8542 (p0) cc_final: 0.8130 (p0) REVERT: B 277 MET cc_start: 0.8457 (ttm) cc_final: 0.8114 (ttp) REVERT: B 280 ARG cc_start: 0.7757 (ptp90) cc_final: 0.6946 (ptm160) REVERT: B 631 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8258 (mp) REVERT: B 645 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7294 (mtm) REVERT: B 677 TRP cc_start: 0.8077 (OUTLIER) cc_final: 0.7128 (p-90) REVERT: B 685 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: C 75 PHE cc_start: 0.5542 (OUTLIER) cc_final: 0.5180 (t80) REVERT: C 243 ASP cc_start: 0.8537 (p0) cc_final: 0.8135 (p0) REVERT: C 280 ARG cc_start: 0.7797 (ptp90) cc_final: 0.6987 (ptm160) REVERT: C 631 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8269 (mp) REVERT: C 645 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7311 (mtt) REVERT: C 677 TRP cc_start: 0.8075 (OUTLIER) cc_final: 0.7137 (p-90) REVERT: D 75 PHE cc_start: 0.5519 (OUTLIER) cc_final: 0.5164 (t80) REVERT: D 243 ASP cc_start: 0.8530 (p0) cc_final: 0.8116 (p0) REVERT: D 280 ARG cc_start: 0.7769 (ptp90) cc_final: 0.6963 (ptm160) REVERT: D 631 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8265 (mp) REVERT: D 645 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7310 (mtt) REVERT: D 677 TRP cc_start: 0.8082 (OUTLIER) cc_final: 0.7152 (p-90) outliers start: 84 outliers final: 55 residues processed: 340 average time/residue: 0.1203 time to fit residues: 66.7197 Evaluate side-chains 347 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 274 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 98 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 212 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** 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 = 0.3876 r_free = 0.3876 target = 0.157480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137110 restraints weight = 24774.216| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.58 r_work: 0.3523 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19788 Z= 0.129 Angle : 0.526 8.743 26868 Z= 0.263 Chirality : 0.037 0.171 3060 Planarity : 0.004 0.050 3324 Dihedral : 7.699 89.292 2684 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.63 % Allowed : 18.85 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.17), residues: 2384 helix: 2.04 (0.14), residues: 1396 sheet: -0.52 (0.55), residues: 112 loop : -1.22 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 193 TYR 0.020 0.001 TYR A 447 PHE 0.013 0.001 PHE B 311 TRP 0.012 0.001 TRP C 677 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (19788) covalent geometry : angle 0.52559 / 0.26 (26868) hydrogen bonds : bond 0.03532 / 2.33 ( 1080) hydrogen bonds : angle 3.68832 / 2.52 ( 3204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 285 time to evaluate : 0.721 Fit side-chains REVERT: A 75 PHE cc_start: 0.5625 (OUTLIER) cc_final: 0.5319 (t80) REVERT: A 243 ASP cc_start: 0.8566 (p0) cc_final: 0.8112 (p0) REVERT: A 280 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7011 (ptm160) REVERT: A 631 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8290 (mp) REVERT: A 645 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7358 (mtm) REVERT: A 677 TRP cc_start: 0.8073 (OUTLIER) cc_final: 0.7034 (p-90) REVERT: A 685 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: B 75 PHE cc_start: 0.5636 (OUTLIER) cc_final: 0.5320 (t80) REVERT: B 243 ASP cc_start: 0.8598 (p0) cc_final: 0.8137 (p0) REVERT: B 269 HIS cc_start: 0.7502 (m90) cc_final: 0.7244 (m90) REVERT: B 277 MET cc_start: 0.8642 (ttm) cc_final: 0.8285 (ttp) REVERT: B 280 ARG cc_start: 0.7738 (ptp90) cc_final: 0.6967 (ptm160) REVERT: B 433 MET cc_start: 0.6908 (mmm) cc_final: 0.6692 (tpp) REVERT: B 531 LYS cc_start: 0.7592 (mmtm) cc_final: 0.7361 (mmtt) REVERT: B 631 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8271 (mp) REVERT: B 645 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7372 (mtm) REVERT: B 677 TRP cc_start: 0.8066 (OUTLIER) cc_final: 0.7063 (p-90) REVERT: B 685 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: C 75 PHE cc_start: 0.5629 (OUTLIER) cc_final: 0.5307 (t80) REVERT: C 243 ASP cc_start: 0.8589 (p0) cc_final: 0.8137 (p0) REVERT: C 280 ARG cc_start: 0.7803 (ptp90) cc_final: 0.7011 (ptm160) REVERT: C 433 MET cc_start: 0.6902 (mmm) cc_final: 0.6690 (tpp) REVERT: C 631 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8306 (mp) REVERT: C 645 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7374 (mtt) REVERT: C 677 TRP cc_start: 0.8093 (OUTLIER) cc_final: 0.7073 (p-90) REVERT: C 685 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: D 75 PHE cc_start: 0.5656 (OUTLIER) cc_final: 0.5335 (t80) REVERT: D 243 ASP cc_start: 0.8602 (p0) cc_final: 0.8127 (p0) REVERT: D 280 ARG cc_start: 0.7773 (ptp90) cc_final: 0.6990 (ptm160) REVERT: D 433 MET cc_start: 0.6913 (mmm) cc_final: 0.6701 (tpp) REVERT: D 631 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8284 (mp) REVERT: D 645 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7321 (mtt) REVERT: D 677 TRP cc_start: 0.8091 (OUTLIER) cc_final: 0.7063 (p-90) REVERT: D 685 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7383 (mp0) outliers start: 94 outliers final: 68 residues processed: 349 average time/residue: 0.1200 time to fit residues: 67.5217 Evaluate side-chains 366 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 278 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 TRP Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 198 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 188 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.159448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.139337 restraints weight = 24743.296| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.58 r_work: 0.3549 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19788 Z= 0.107 Angle : 0.506 8.746 26868 Z= 0.254 Chirality : 0.036 0.170 3060 Planarity : 0.004 0.051 3324 Dihedral : 7.566 89.898 2684 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.28 % Allowed : 19.44 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.17), residues: 2384 helix: 2.18 (0.14), residues: 1396 sheet: -0.41 (0.55), residues: 112 loop : -1.17 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 193 TYR 0.019 0.001 TYR B 447 PHE 0.011 0.001 PHE A 311 TRP 0.011 0.001 TRP C 677 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (19788) covalent geometry : angle 0.50585 / 0.25 (26868) hydrogen bonds : bond 0.03287 / 2.17 ( 1080) hydrogen bonds : angle 3.63290 / 2.48 ( 3204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 295 time to evaluate : 0.713 Fit side-chains REVERT: A 75 PHE cc_start: 0.5486 (OUTLIER) cc_final: 0.5075 (t80) REVERT: A 243 ASP cc_start: 0.8484 (p0) cc_final: 0.7942 (p0) REVERT: A 280 ARG cc_start: 0.7787 (ptp90) cc_final: 0.6958 (ptm160) REVERT: A 296 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8319 (mt) REVERT: A 631 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8283 (mp) REVERT: A 645 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7351 (mtt) REVERT: A 677 TRP cc_start: 0.8064 (OUTLIER) cc_final: 0.7028 (p-90) REVERT: A 685 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: B 75 PHE cc_start: 0.5423 (OUTLIER) cc_final: 0.5004 (t80) REVERT: B 243 ASP cc_start: 0.8491 (p0) cc_final: 0.7946 (p0) REVERT: B 280 ARG cc_start: 0.7791 (ptp90) cc_final: 0.7030 (ptm160) REVERT: B 631 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8258 (mp) REVERT: B 645 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7361 (mtm) REVERT: B 677 TRP cc_start: 0.8062 (OUTLIER) cc_final: 0.7023 (p-90) REVERT: B 685 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: C 75 PHE cc_start: 0.5460 (OUTLIER) cc_final: 0.5027 (t80) REVERT: C 243 ASP cc_start: 0.8468 (p0) cc_final: 0.7956 (p0) REVERT: C 280 ARG cc_start: 0.7826 (ptp90) cc_final: 0.7039 (ptm160) REVERT: C 631 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8272 (mp) REVERT: C 645 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7341 (mtt) REVERT: C 677 TRP cc_start: 0.8072 (OUTLIER) cc_final: 0.7131 (p-90) REVERT: C 685 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: D 75 PHE cc_start: 0.5428 (OUTLIER) cc_final: 0.5013 (t80) REVERT: D 243 ASP cc_start: 0.8474 (p0) cc_final: 0.7966 (p0) REVERT: D 631 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8270 (mp) REVERT: D 645 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7338 (mtt) REVERT: D 677 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.7147 (p-90) REVERT: D 685 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7333 (mp0) outliers start: 87 outliers final: 59 residues processed: 351 average time/residue: 0.1156 time to fit residues: 66.3082 Evaluate side-chains 358 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 278 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 TRP Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 33 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.153357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132943 restraints weight = 25126.300| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.63 r_work: 0.3465 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19788 Z= 0.224 Angle : 0.630 8.793 26868 Z= 0.317 Chirality : 0.041 0.176 3060 Planarity : 0.005 0.051 3324 Dihedral : 7.590 85.840 2682 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.68 % Allowed : 19.64 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2384 helix: 1.72 (0.13), residues: 1396 sheet: -0.71 (0.55), residues: 112 loop : -1.27 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 193 TYR 0.023 0.002 TYR D 343 PHE 0.018 0.002 PHE B 311 TRP 0.016 0.001 TRP B 677 HIS 0.006 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.22 (19788) covalent geometry : angle 0.63037 / 0.32 (26868) hydrogen bonds : bond 0.04184 / 2.75 ( 1080) hydrogen bonds : angle 3.88578 / 2.66 ( 3204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 283 time to evaluate : 0.669 Fit side-chains REVERT: A 75 PHE cc_start: 0.5677 (OUTLIER) cc_final: 0.5460 (t80) REVERT: A 631 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8281 (mp) REVERT: A 645 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7256 (mtm) REVERT: A 677 TRP cc_start: 0.8145 (OUTLIER) cc_final: 0.7452 (p-90) REVERT: A 685 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: B 75 PHE cc_start: 0.5616 (OUTLIER) cc_final: 0.5375 (t80) REVERT: B 269 HIS cc_start: 0.7572 (m90) cc_final: 0.7354 (m90) REVERT: B 631 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8273 (mp) REVERT: B 645 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7287 (mtm) REVERT: B 677 TRP cc_start: 0.8132 (OUTLIER) cc_final: 0.7348 (p-90) REVERT: B 685 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: C 75 PHE cc_start: 0.5664 (OUTLIER) cc_final: 0.5396 (t80) REVERT: C 631 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8265 (mp) REVERT: C 645 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7336 (mtm) REVERT: C 677 TRP cc_start: 0.8157 (OUTLIER) cc_final: 0.7293 (p-90) REVERT: C 685 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: D 75 PHE cc_start: 0.5667 (OUTLIER) cc_final: 0.5443 (t80) REVERT: D 280 ARG cc_start: 0.7722 (ptp90) cc_final: 0.6948 (ptm160) REVERT: D 631 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8276 (mp) REVERT: D 645 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7263 (mtt) REVERT: D 677 TRP cc_start: 0.8169 (OUTLIER) cc_final: 0.7304 (p-90) REVERT: D 685 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7522 (mp0) outliers start: 95 outliers final: 65 residues processed: 343 average time/residue: 0.1130 time to fit residues: 63.1990 Evaluate side-chains 348 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 263 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 TRP Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 229 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.157166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137187 restraints weight = 24960.786| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.49 r_work: 0.3519 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19788 Z= 0.126 Angle : 0.541 8.656 26868 Z= 0.273 Chirality : 0.037 0.176 3060 Planarity : 0.004 0.052 3324 Dihedral : 7.494 88.060 2682 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.08 % Allowed : 20.28 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.17), residues: 2384 helix: 2.01 (0.14), residues: 1396 sheet: -0.67 (0.54), residues: 112 loop : -1.21 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 193 TYR 0.019 0.002 TYR C 447 PHE 0.011 0.001 PHE B 311 TRP 0.012 0.001 TRP B 677 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (19788) covalent geometry : angle 0.54118 / 0.27 (26868) hydrogen bonds : bond 0.03545 / 2.34 ( 1080) hydrogen bonds : angle 3.71013 / 2.53 ( 3204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 274 time to evaluate : 0.763 Fit side-chains REVERT: A 81 PHE cc_start: 0.6868 (m-80) cc_final: 0.6650 (m-80) REVERT: A 243 ASP cc_start: 0.8645 (p0) cc_final: 0.8266 (p0) REVERT: A 280 ARG cc_start: 0.7810 (ptp90) cc_final: 0.7013 (ptm160) REVERT: A 631 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8276 (mp) REVERT: A 645 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7325 (mtt) REVERT: A 677 TRP cc_start: 0.8075 (OUTLIER) cc_final: 0.6993 (p-90) REVERT: A 685 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: B 81 PHE cc_start: 0.6897 (m-80) cc_final: 0.6677 (m-80) REVERT: B 243 ASP cc_start: 0.8643 (p0) cc_final: 0.8368 (p0) REVERT: B 280 ARG cc_start: 0.7753 (ptp90) cc_final: 0.6961 (ptm160) REVERT: B 631 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8264 (mp) REVERT: B 645 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7350 (mtt) REVERT: B 677 TRP cc_start: 0.8064 (OUTLIER) cc_final: 0.7005 (p-90) REVERT: B 685 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: C 81 PHE cc_start: 0.6874 (m-80) cc_final: 0.6661 (m-80) REVERT: C 243 ASP cc_start: 0.8655 (p0) cc_final: 0.8240 (p0) REVERT: C 280 ARG cc_start: 0.7809 (ptp90) cc_final: 0.7045 (ptm160) REVERT: C 631 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8269 (mp) REVERT: C 645 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7344 (mtt) REVERT: C 677 TRP cc_start: 0.8046 (OUTLIER) cc_final: 0.6921 (p-90) REVERT: C 685 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: D 81 PHE cc_start: 0.6895 (m-80) cc_final: 0.6666 (m-80) REVERT: D 243 ASP cc_start: 0.8653 (p0) cc_final: 0.8367 (p0) REVERT: D 280 ARG cc_start: 0.7865 (ptp90) cc_final: 0.7073 (ptm160) REVERT: D 631 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8267 (mp) REVERT: D 645 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7292 (mtt) REVERT: D 677 TRP cc_start: 0.8052 (OUTLIER) cc_final: 0.6924 (p-90) REVERT: D 685 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7423 (mp0) outliers start: 83 outliers final: 56 residues processed: 333 average time/residue: 0.1194 time to fit residues: 65.2055 Evaluate side-chains 339 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 267 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 TRP Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 231 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 228 optimal weight: 0.3980 chunk 235 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.159447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.139435 restraints weight = 24827.913| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.53 r_work: 0.3556 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19788 Z= 0.107 Angle : 0.520 8.439 26868 Z= 0.263 Chirality : 0.037 0.179 3060 Planarity : 0.004 0.053 3324 Dihedral : 7.371 89.796 2676 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.74 % Allowed : 20.57 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.17), residues: 2384 helix: 2.19 (0.14), residues: 1396 sheet: -0.75 (0.52), residues: 112 loop : -1.19 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 193 TYR 0.019 0.001 TYR C 447 PHE 0.010 0.001 PHE D 311 TRP 0.023 0.001 TRP A 223 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (19788) covalent geometry : angle 0.52038 / 0.26 (26868) hydrogen bonds : bond 0.03320 / 2.20 ( 1080) hydrogen bonds : angle 3.67436 / 2.51 ( 3204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4007.19 seconds wall clock time: 69 minutes 39.86 seconds (4179.86 seconds total)