Starting phenix.real_space_refine on Thu Sep 18 18:19:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wkn_21705/09_2025/6wkn_21705.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wkn_21705/09_2025/6wkn_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_2025/6wkn_21705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wkn_21705/09_2025/6wkn_21705.map" model { file = "/net/cci-nas-00/data/ceres_data/6wkn_21705/09_2025/6wkn_21705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wkn_21705/09_2025/6wkn_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-2.0-5805/lib/python3.9/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: 4.56, per 1000 atoms: 0.24 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: 1.85 Conformation dependent library (CDL) restraints added in 810.4 milliseconds Enol-peptide restraints added in 1.7 microseconds 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: 0.59 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: 3.23 Time building geometry restraints manager: 2.39 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: 10285 16.51 - 33.02: 907 33.02 - 49.54: 276 49.54 - 66.05: 88 66.05 - 82.56: 40 Dihedral angle restraints: 11596 sinusoidal: 4516 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 11593 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: 0.05 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.140 Find NCS groups from input model: 0.160 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 15.690 82.559 7020 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 aren 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 covalent geometry : bond 0.00654 (19788) covalent geometry : angle 0.73817 (26868) hydrogen bonds : bond 0.14391 ( 1080) hydrogen bonds : angle 6.30728 ( 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 : 0.768 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: 0.7979 (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: 0.1490 time to fit residues: 117.7159 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 : 0.684 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.157609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137086 restraints weight = 25062.305| |-----------------------------------------------------------------------------| 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: 0.3394 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2002 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 6.783 26868 Z= 0.281 Chirality : 0.038 0.122 3060 Planarity : 0.005 0.046 3324 Dihedral : 9.109 89.210 2762 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.43 % Allowed : 14.96 % Favored : 80.61 % 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 aren not related in a simple way. whole: -0.82 (0.16), residues: 2384 helix: 0.39 (0.13), residues: 1424 sheet: -1.57 (0.49), residues: 112 loop : -1.98 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 619 TYR 0.014 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 A 251 Details of bonding type rmsd covalent geometry : bond 0.00325 (19788) covalent geometry : angle 0.54286 (26868) hydrogen bonds : bond 0.04081 ( 1080) hydrogen bonds : angle 4.04478 ( 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 397 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 307 time to evaluate : 0.752 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: 0.8774 (tp) cc_final: 0.8530 (mt) REVERT: A 243 ASP cc_start: 0.8466 (p0) cc_final: 0.8077 (p0) REVERT: A 269 HIS cc_start: 0.7466 (m90) cc_final: 0.7201 (m90) REVERT: A 277 MET cc_start: 0.8529 (ttm) cc_final: 0.8308 (ttp) REVERT: A 368 ASN cc_start: 0.8255 (p0) cc_final: 0.7972 (p0) REVERT: A 412 TYR cc_start: 0.7587 (t80) cc_final: 0.7370 (t80) REVERT: A 631 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 634 TYR cc_start: 0.8421 (t80) cc_final: 0.8193 (t80) REVERT: A 638 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8126 (mp) REVERT: A 645 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7239 (mtm) REVERT: A 677 TRP cc_start: 0.8026 (OUTLIER) cc_final: 0.7014 (p-90) REVERT: A 685 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7919 (mm-30) REVERT: B 183 LEU cc_start: 0.8764 (tp) cc_final: 0.8514 (mt) REVERT: B 243 ASP cc_start: 0.8438 (p0) cc_final: 0.8054 (p0) REVERT: B 269 HIS cc_start: 0.7487 (m90) cc_final: 0.7214 (m90) REVERT: B 277 MET cc_start: 0.8492 (ttm) cc_final: 0.8273 (ttp) REVERT: B 368 ASN cc_start: 0.8273 (p0) cc_final: 0.7988 (p0) REVERT: B 412 TYR cc_start: 0.7582 (t80) cc_final: 0.7354 (t80) REVERT: B 631 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8290 (mp) REVERT: B 634 TYR cc_start: 0.8430 (t80) cc_final: 0.8200 (t80) REVERT: B 638 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8091 (mp) REVERT: B 645 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7247 (mtm) REVERT: B 677 TRP cc_start: 0.8023 (OUTLIER) cc_final: 0.6931 (p-90) REVERT: B 685 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7966 (mm-30) REVERT: C 183 LEU cc_start: 0.8779 (tp) cc_final: 0.8519 (mt) REVERT: C 243 ASP cc_start: 0.8473 (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: 0.8491 (ttm) cc_final: 0.8278 (ttp) REVERT: C 368 ASN cc_start: 0.8237 (p0) cc_final: 0.7957 (p0) REVERT: C 412 TYR cc_start: 0.7602 (t80) cc_final: 0.7382 (t80) REVERT: C 631 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8289 (mp) REVERT: C 634 TYR cc_start: 0.8419 (t80) cc_final: 0.8190 (t80) REVERT: C 638 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8125 (mp) REVERT: C 645 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7265 (mtm) REVERT: C 677 TRP cc_start: 0.8017 (OUTLIER) cc_final: 0.6927 (p-90) REVERT: C 685 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7958 (mm-30) REVERT: D 183 LEU cc_start: 0.8754 (tp) cc_final: 0.8503 (mt) REVERT: D 243 ASP cc_start: 0.8451 (p0) cc_final: 0.7897 (p0) REVERT: D 269 HIS cc_start: 0.7469 (m90) cc_final: 0.7201 (m90) REVERT: D 277 MET cc_start: 0.8517 (ttm) cc_final: 0.8289 (ttp) REVERT: D 368 ASN cc_start: 0.8259 (p0) cc_final: 0.7973 (p0) REVERT: D 412 TYR cc_start: 0.7609 (t80) cc_final: 0.7374 (t80) REVERT: D 631 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8299 (mp) REVERT: D 634 TYR cc_start: 0.8447 (t80) cc_final: 0.8215 (t80) REVERT: D 638 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8097 (mp) REVERT: D 645 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7259 (mtm) REVERT: D 677 TRP cc_start: 0.8026 (OUTLIER) cc_final: 0.6945 (p-90) REVERT: D 685 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7963 (mm-30) outliers start: 90 outliers final: 59 residues processed: 363 average time/residue: 0.1312 time to fit residues: 75.9063 Evaluate side-chains 333 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 254 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 137 MET Chi-restraints excluded: chain A residue 158 THR 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 137 MET 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 137 MET 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 137 MET 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: 9.9990 chunk 65 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 173 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 639 ASN ** 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 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.159747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.139892 restraints weight = 24852.135| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.45 r_work: 0.3551 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19788 Z= 0.109 Angle : 0.494 7.258 26868 Z= 0.253 Chirality : 0.036 0.167 3060 Planarity : 0.004 0.037 3324 Dihedral : 8.071 89.370 2724 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.49 % Allowed : 16.14 % Favored : 80.36 % 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 aren not related in a simple way. whole: 0.13 (0.17), residues: 2384 helix: 1.24 (0.13), residues: 1428 sheet: -1.29 (0.50), residues: 112 loop : -1.76 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 193 TYR 0.010 0.001 TYR A 98 PHE 0.013 0.001 PHE A 311 TRP 0.010 0.001 TRP A 677 HIS 0.002 0.001 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00245 (19788) covalent geometry : angle 0.49374 (26868) hydrogen bonds : bond 0.03582 ( 1080) hydrogen bonds : angle 3.76753 ( 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 367 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 296 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8328 (mt) cc_final: 0.8123 (tp) REVERT: A 183 LEU cc_start: 0.8704 (tp) cc_final: 0.8484 (mt) REVERT: A 193 ARG cc_start: 0.7911 (tpp80) cc_final: 0.7609 (tpp80) REVERT: A 243 ASP cc_start: 0.8462 (p0) cc_final: 0.7901 (p0) REVERT: A 269 HIS cc_start: 0.7366 (m90) cc_final: 0.7119 (m90) REVERT: A 277 MET cc_start: 0.8423 (ttm) cc_final: 0.8213 (ttp) REVERT: A 368 ASN cc_start: 0.8175 (p0) cc_final: 0.7941 (p0) REVERT: A 468 MET cc_start: 0.6895 (mtm) cc_final: 0.6309 (mtm) REVERT: A 631 LEU cc_start: 0.8690 (tt) cc_final: 0.8262 (mp) REVERT: A 645 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7327 (mtm) REVERT: A 677 TRP cc_start: 0.8015 (OUTLIER) cc_final: 0.6858 (p-90) REVERT: A 685 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7903 (mm-30) REVERT: B 183 LEU cc_start: 0.8713 (tp) cc_final: 0.8486 (mt) REVERT: B 193 ARG cc_start: 0.7824 (tpp80) cc_final: 0.7583 (tpp80) REVERT: B 243 ASP cc_start: 0.8435 (p0) cc_final: 0.7876 (p0) REVERT: B 269 HIS cc_start: 0.7347 (m90) cc_final: 0.7101 (m90) REVERT: B 277 MET cc_start: 0.8431 (ttm) cc_final: 0.8224 (ttp) REVERT: B 368 ASN cc_start: 0.8205 (p0) cc_final: 0.7968 (p0) REVERT: B 412 TYR cc_start: 0.7489 (t80) cc_final: 0.7260 (t80) REVERT: B 533 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7220 (tt) REVERT: B 631 LEU cc_start: 0.8682 (tt) cc_final: 0.8254 (mp) REVERT: B 638 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8191 (mp) REVERT: B 645 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7361 (mtm) REVERT: B 677 TRP cc_start: 0.8005 (OUTLIER) cc_final: 0.6881 (p-90) REVERT: C 183 LEU cc_start: 0.8716 (tp) cc_final: 0.8484 (mt) REVERT: C 193 ARG cc_start: 0.7824 (tpp80) cc_final: 0.7586 (tpp80) REVERT: C 243 ASP cc_start: 0.8442 (p0) cc_final: 0.7901 (p0) REVERT: C 269 HIS cc_start: 0.7390 (m90) cc_final: 0.7138 (m90) REVERT: C 277 MET cc_start: 0.8408 (ttm) cc_final: 0.8200 (ttp) REVERT: C 368 ASN cc_start: 0.8174 (p0) cc_final: 0.7943 (p0) REVERT: C 412 TYR cc_start: 0.7529 (t80) cc_final: 0.7313 (t80) REVERT: C 468 MET cc_start: 0.6893 (mtm) cc_final: 0.6310 (mtm) REVERT: C 631 LEU cc_start: 0.8688 (tt) cc_final: 0.8260 (mp) REVERT: C 645 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7343 (mtm) REVERT: C 677 TRP cc_start: 0.8020 (OUTLIER) cc_final: 0.6881 (p-90) REVERT: D 183 LEU cc_start: 0.8718 (tp) cc_final: 0.8487 (mt) REVERT: D 193 ARG cc_start: 0.7837 (tpp80) cc_final: 0.7596 (tpp80) REVERT: D 243 ASP cc_start: 0.8457 (p0) cc_final: 0.7901 (p0) REVERT: D 269 HIS cc_start: 0.7383 (m90) cc_final: 0.7133 (m90) REVERT: D 277 MET cc_start: 0.8439 (ttm) cc_final: 0.8223 (ttp) REVERT: D 368 ASN cc_start: 0.8193 (p0) cc_final: 0.7958 (p0) REVERT: D 412 TYR cc_start: 0.7507 (t80) cc_final: 0.7279 (t80) REVERT: D 533 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7189 (tt) REVERT: D 631 LEU cc_start: 0.8691 (tt) cc_final: 0.8271 (mp) REVERT: D 638 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8192 (mp) REVERT: D 645 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7368 (mtm) REVERT: D 677 TRP cc_start: 0.8013 (OUTLIER) cc_final: 0.6918 (p-90) outliers start: 71 outliers final: 38 residues processed: 344 average time/residue: 0.1252 time to fit residues: 67.3668 Evaluate side-chains 319 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 268 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 254 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 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 645 MET Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 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 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 638 LEU Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 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 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 645 MET Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 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 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 638 LEU Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 677 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 138 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 222 GLN ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 263 ASN ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 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 = 0.3890 r_free = 0.3890 target = 0.158490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.138169 restraints weight = 24926.698| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.47 r_work: 0.3533 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19788 Z= 0.122 Angle : 0.502 6.726 26868 Z= 0.256 Chirality : 0.036 0.118 3060 Planarity : 0.004 0.036 3324 Dihedral : 7.590 88.603 2699 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.58 % Allowed : 16.34 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.17), residues: 2384 helix: 1.59 (0.14), residues: 1428 sheet: -1.05 (0.52), residues: 112 loop : -1.66 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 193 TYR 0.017 0.001 TYR B 98 PHE 0.014 0.001 PHE A 311 TRP 0.011 0.001 TRP A 677 HIS 0.002 0.001 HIS D 370 Details of bonding type rmsd covalent geometry : bond 0.00281 (19788) covalent geometry : angle 0.50209 (26868) hydrogen bonds : bond 0.03547 ( 1080) hydrogen bonds : angle 3.68808 ( 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 369 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 276 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.5110 (OUTLIER) cc_final: 0.4233 (t80) REVERT: A 193 ARG cc_start: 0.7911 (tpp80) cc_final: 0.7657 (tpp80) REVERT: A 243 ASP cc_start: 0.8520 (p0) cc_final: 0.8058 (p0) REVERT: A 277 MET cc_start: 0.8491 (ttm) cc_final: 0.8257 (ttp) REVERT: A 631 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8290 (mp) REVERT: A 645 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7336 (mtm) REVERT: A 677 TRP cc_start: 0.8044 (OUTLIER) cc_final: 0.6986 (p-90) REVERT: A 685 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: B 80 LEU cc_start: 0.8651 (tp) cc_final: 0.8438 (mt) REVERT: B 243 ASP cc_start: 0.8525 (p0) cc_final: 0.8112 (p0) REVERT: B 277 MET cc_start: 0.8441 (ttm) cc_final: 0.8212 (ttp) REVERT: B 412 TYR cc_start: 0.7560 (t80) cc_final: 0.7123 (t80) REVERT: B 533 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.7209 (tt) REVERT: B 631 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8251 (mp) REVERT: B 645 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7337 (mtm) REVERT: B 677 TRP cc_start: 0.8039 (OUTLIER) cc_final: 0.7022 (p-90) REVERT: C 80 LEU cc_start: 0.8650 (tp) cc_final: 0.8428 (mt) REVERT: C 243 ASP cc_start: 0.8542 (p0) cc_final: 0.8118 (p0) REVERT: C 277 MET cc_start: 0.8409 (ttm) cc_final: 0.8178 (ttp) REVERT: C 412 TYR cc_start: 0.7578 (t80) cc_final: 0.7158 (t80) REVERT: C 631 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8271 (mp) REVERT: C 645 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7340 (mtm) REVERT: C 677 TRP cc_start: 0.8051 (OUTLIER) cc_final: 0.7012 (p-90) REVERT: D 80 LEU cc_start: 0.8656 (tp) cc_final: 0.8427 (mt) REVERT: D 243 ASP cc_start: 0.8532 (p0) cc_final: 0.8106 (p0) REVERT: D 277 MET cc_start: 0.8492 (ttm) cc_final: 0.8248 (ttp) REVERT: D 412 TYR cc_start: 0.7579 (t80) cc_final: 0.7138 (t80) REVERT: D 533 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7194 (tt) REVERT: D 631 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8277 (mp) REVERT: D 645 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7331 (mtm) REVERT: D 677 TRP cc_start: 0.8033 (OUTLIER) cc_final: 0.7048 (p-90) outliers start: 93 outliers final: 62 residues processed: 335 average time/residue: 0.1282 time to fit residues: 68.5029 Evaluate side-chains 337 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 259 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 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 112 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 222 GLN 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 533 ILE 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 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 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 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 171 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 127 optimal weight: 0.0050 chunk 238 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 119 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 263 ASN ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3882 r_free = 0.3882 target = 0.157612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.137388 restraints weight = 24955.875| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.44 r_work: 0.3526 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19788 Z= 0.134 Angle : 0.508 6.279 26868 Z= 0.260 Chirality : 0.037 0.146 3060 Planarity : 0.004 0.045 3324 Dihedral : 7.596 88.003 2695 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.48 % Allowed : 17.32 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.17), residues: 2384 helix: 1.79 (0.14), residues: 1420 sheet: -0.92 (0.52), residues: 112 loop : -1.59 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 684 TYR 0.013 0.001 TYR D 98 PHE 0.014 0.001 PHE A 311 TRP 0.012 0.001 TRP D 677 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00315 (19788) covalent geometry : angle 0.50791 (26868) hydrogen bonds : bond 0.03592 ( 1080) hydrogen bonds : angle 3.68625 ( 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 372 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 281 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.5217 (OUTLIER) cc_final: 0.4527 (t80) REVERT: A 243 ASP cc_start: 0.8572 (p0) cc_final: 0.8133 (p0) REVERT: A 277 MET cc_start: 0.8528 (ttm) cc_final: 0.8281 (ttp) REVERT: A 296 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8408 (mt) REVERT: A 631 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8294 (mp) REVERT: A 634 TYR cc_start: 0.8377 (t80) cc_final: 0.8168 (t80) REVERT: A 638 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 645 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7343 (mtm) REVERT: A 677 TRP cc_start: 0.8067 (OUTLIER) cc_final: 0.7027 (p-90) REVERT: B 80 LEU cc_start: 0.8718 (tp) cc_final: 0.8431 (mt) REVERT: B 243 ASP cc_start: 0.8569 (p0) cc_final: 0.8112 (p0) REVERT: B 277 MET cc_start: 0.8500 (ttm) cc_final: 0.8229 (ttp) REVERT: B 296 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8402 (mt) REVERT: B 412 TYR cc_start: 0.7474 (t80) cc_final: 0.7176 (t80) REVERT: B 631 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8264 (mp) REVERT: B 645 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7354 (mtm) REVERT: B 677 TRP cc_start: 0.8050 (OUTLIER) cc_final: 0.7060 (p-90) REVERT: C 80 LEU cc_start: 0.8718 (tp) cc_final: 0.8429 (mt) REVERT: C 243 ASP cc_start: 0.8565 (p0) cc_final: 0.8131 (p0) REVERT: C 277 MET cc_start: 0.8506 (ttm) cc_final: 0.8272 (ttp) REVERT: C 296 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8401 (mt) REVERT: C 412 TYR cc_start: 0.7526 (t80) cc_final: 0.7074 (t80) REVERT: C 631 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8284 (mp) REVERT: C 638 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8045 (mp) REVERT: C 645 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7341 (mtm) REVERT: C 677 TRP cc_start: 0.8060 (OUTLIER) cc_final: 0.7045 (p-90) REVERT: D 80 LEU cc_start: 0.8730 (tp) cc_final: 0.8428 (mt) REVERT: D 243 ASP cc_start: 0.8557 (p0) cc_final: 0.8101 (p0) REVERT: D 277 MET cc_start: 0.8559 (ttm) cc_final: 0.8312 (ttp) REVERT: D 412 TYR cc_start: 0.7531 (t80) cc_final: 0.7057 (t80) REVERT: D 533 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7166 (tt) REVERT: D 631 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8269 (mp) REVERT: D 645 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7361 (mtm) REVERT: D 677 TRP cc_start: 0.8060 (OUTLIER) cc_final: 0.7064 (p-90) outliers start: 91 outliers final: 67 residues processed: 341 average time/residue: 0.1163 time to fit residues: 63.6424 Evaluate side-chains 354 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 268 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 126 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 296 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 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 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 669 LEU Chi-restraints excluded: chain A residue 677 TRP 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 112 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 296 LEU 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 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 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 296 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 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 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 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 112 THR 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 67 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 48 optimal weight: 0.2980 chunk 128 optimal weight: 7.9990 chunk 203 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 220 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 = 0.3899 r_free = 0.3899 target = 0.159222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138587 restraints weight = 24695.700| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.55 r_work: 0.3551 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2925 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= 0.110 Angle : 0.494 7.936 26868 Z= 0.252 Chirality : 0.036 0.145 3060 Planarity : 0.004 0.049 3324 Dihedral : 7.588 89.071 2692 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.04 % Allowed : 18.41 % Favored : 77.56 % 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 aren not related in a simple way. whole: 1.17 (0.17), residues: 2384 helix: 2.10 (0.14), residues: 1396 sheet: -0.72 (0.52), residues: 112 loop : -1.26 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 193 TYR 0.019 0.001 TYR A 447 PHE 0.012 0.001 PHE D 311 TRP 0.011 0.001 TRP C 677 HIS 0.002 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00249 (19788) covalent geometry : angle 0.49421 (26868) hydrogen bonds : bond 0.03360 ( 1080) hydrogen bonds : angle 3.63300 ( 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 367 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 285 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.5181 (OUTLIER) cc_final: 0.4172 (t80) REVERT: A 243 ASP cc_start: 0.8517 (p0) cc_final: 0.8100 (p0) REVERT: A 277 MET cc_start: 0.8494 (ttm) cc_final: 0.8193 (ttp) REVERT: A 280 ARG cc_start: 0.7816 (ptp90) cc_final: 0.6982 (ptm160) REVERT: A 296 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8364 (mt) REVERT: A 631 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 645 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7311 (mtm) REVERT: A 677 TRP cc_start: 0.8029 (OUTLIER) cc_final: 0.7020 (p-90) REVERT: B 80 LEU cc_start: 0.8765 (tp) cc_final: 0.8466 (mt) REVERT: B 243 ASP cc_start: 0.8519 (p0) cc_final: 0.8112 (p0) REVERT: B 277 MET cc_start: 0.8466 (ttm) cc_final: 0.8156 (ttp) REVERT: B 280 ARG cc_start: 0.7785 (ptp90) cc_final: 0.6960 (ptm160) REVERT: B 296 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8356 (mt) REVERT: B 631 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8258 (mp) REVERT: B 645 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7315 (mtm) REVERT: B 677 TRP cc_start: 0.8042 (OUTLIER) cc_final: 0.7075 (p-90) REVERT: C 243 ASP cc_start: 0.8507 (p0) cc_final: 0.8123 (p0) REVERT: C 277 MET cc_start: 0.8443 (ttm) cc_final: 0.8169 (ttp) REVERT: C 280 ARG cc_start: 0.7753 (ptp90) cc_final: 0.6956 (ptm160) REVERT: C 296 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8353 (mt) REVERT: C 631 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8278 (mp) REVERT: C 645 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7296 (mtm) REVERT: C 677 TRP cc_start: 0.8044 (OUTLIER) cc_final: 0.7057 (p-90) REVERT: D 80 LEU cc_start: 0.8774 (tp) cc_final: 0.8458 (mt) REVERT: D 243 ASP cc_start: 0.8511 (p0) cc_final: 0.7985 (p0) REVERT: D 277 MET cc_start: 0.8434 (ttm) cc_final: 0.8189 (ttp) REVERT: D 280 ARG cc_start: 0.7723 (ptp90) cc_final: 0.6930 (ptm160) REVERT: D 296 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8364 (mt) REVERT: D 533 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7160 (tt) REVERT: D 631 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8281 (mp) REVERT: D 645 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7299 (mtm) REVERT: D 677 TRP cc_start: 0.8044 (OUTLIER) cc_final: 0.7075 (p-90) outliers start: 82 outliers final: 57 residues processed: 344 average time/residue: 0.1252 time to fit residues: 68.9292 Evaluate side-chains 350 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 275 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 254 VAL Chi-restraints excluded: chain A residue 296 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 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 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 296 LEU 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 528 MET 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 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 296 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 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 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 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 296 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 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 533 ILE 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: 2.9990 chunk 160 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.155090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134944 restraints weight = 25018.319| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.40 r_work: 0.3487 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19788 Z= 0.186 Angle : 0.574 7.998 26868 Z= 0.292 Chirality : 0.039 0.172 3060 Planarity : 0.005 0.049 3324 Dihedral : 7.727 86.283 2692 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.53 % Allowed : 18.11 % Favored : 77.36 % 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 aren not related in a simple way. whole: 0.92 (0.17), residues: 2384 helix: 1.83 (0.13), residues: 1396 sheet: -0.71 (0.54), residues: 112 loop : -1.27 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 684 TYR 0.019 0.002 TYR B 343 PHE 0.017 0.001 PHE C 311 TRP 0.015 0.001 TRP B 677 HIS 0.004 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00444 (19788) covalent geometry : angle 0.57413 (26868) hydrogen bonds : bond 0.03959 ( 1080) hydrogen bonds : angle 3.81539 ( 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 369 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 277 time to evaluate : 0.770 Fit side-chains REVERT: A 75 PHE cc_start: 0.5454 (OUTLIER) cc_final: 0.4818 (t80) REVERT: A 243 ASP cc_start: 0.8676 (p0) cc_final: 0.8224 (p0) REVERT: A 277 MET cc_start: 0.8571 (ttm) cc_final: 0.8325 (ttp) REVERT: A 412 TYR cc_start: 0.7526 (t80) cc_final: 0.7047 (t80) REVERT: A 631 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8314 (mp) REVERT: A 638 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 645 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7284 (mtm) REVERT: A 677 TRP cc_start: 0.8088 (OUTLIER) cc_final: 0.7272 (p-90) REVERT: B 80 LEU cc_start: 0.8791 (tp) cc_final: 0.8519 (mt) REVERT: B 243 ASP cc_start: 0.8681 (p0) cc_final: 0.8215 (p0) REVERT: B 277 MET cc_start: 0.8562 (ttm) cc_final: 0.8284 (ttp) REVERT: B 296 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8478 (mt) REVERT: B 631 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 645 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7302 (mtm) REVERT: B 677 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7299 (p-90) REVERT: C 243 ASP cc_start: 0.8686 (p0) cc_final: 0.8233 (p0) REVERT: C 277 MET cc_start: 0.8591 (ttm) cc_final: 0.8330 (ttp) REVERT: C 296 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8482 (mt) REVERT: C 631 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8289 (mp) REVERT: C 638 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8115 (mp) REVERT: C 645 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7281 (mtm) REVERT: C 677 TRP cc_start: 0.8115 (OUTLIER) cc_final: 0.7296 (p-90) REVERT: D 80 LEU cc_start: 0.8791 (tp) cc_final: 0.8506 (mt) REVERT: D 243 ASP cc_start: 0.8675 (p0) cc_final: 0.8206 (p0) REVERT: D 277 MET cc_start: 0.8602 (ttm) cc_final: 0.8344 (ttp) REVERT: D 533 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7156 (tt) REVERT: D 631 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8286 (mp) REVERT: D 645 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7282 (mtm) REVERT: D 677 TRP cc_start: 0.8109 (OUTLIER) cc_final: 0.7311 (p-90) outliers start: 92 outliers final: 65 residues processed: 340 average time/residue: 0.1300 time to fit residues: 71.7541 Evaluate side-chains 343 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 260 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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 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 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 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 296 LEU 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 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 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 296 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 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 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 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 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 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 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 669 LEU Chi-restraints excluded: chain D residue 677 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 198 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 178 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 225 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.159051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138463 restraints weight = 24786.217| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.56 r_work: 0.3545 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19788 Z= 0.108 Angle : 0.502 7.279 26868 Z= 0.254 Chirality : 0.037 0.161 3060 Planarity : 0.004 0.052 3324 Dihedral : 7.549 89.150 2692 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.74 % Allowed : 19.24 % Favored : 77.02 % 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 aren not related in a simple way. whole: 1.28 (0.17), residues: 2384 helix: 2.14 (0.14), residues: 1396 sheet: -0.56 (0.55), residues: 112 loop : -1.16 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 193 TYR 0.018 0.001 TYR A 447 PHE 0.011 0.001 PHE A 311 TRP 0.012 0.001 TRP C 677 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00245 (19788) covalent geometry : angle 0.50236 (26868) hydrogen bonds : bond 0.03340 ( 1080) hydrogen bonds : angle 3.64841 ( 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 354 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 278 time to evaluate : 0.722 Fit side-chains REVERT: A 75 PHE cc_start: 0.5428 (OUTLIER) cc_final: 0.4799 (t80) REVERT: A 243 ASP cc_start: 0.8520 (p0) cc_final: 0.8119 (p0) REVERT: A 277 MET cc_start: 0.8472 (ttm) cc_final: 0.8182 (ttp) REVERT: A 280 ARG cc_start: 0.7799 (ptp90) cc_final: 0.6999 (ptm160) REVERT: A 631 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8260 (mp) REVERT: A 645 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7305 (mtm) REVERT: A 677 TRP cc_start: 0.8015 (OUTLIER) cc_final: 0.7054 (p-90) REVERT: B 77 ARG cc_start: 0.7261 (ttm170) cc_final: 0.6959 (ttp80) REVERT: B 80 LEU cc_start: 0.8767 (tp) cc_final: 0.8512 (mt) REVERT: B 243 ASP cc_start: 0.8545 (p0) cc_final: 0.8148 (p0) REVERT: B 277 MET cc_start: 0.8431 (ttm) cc_final: 0.8175 (ttp) REVERT: B 280 ARG cc_start: 0.7783 (ptp90) cc_final: 0.6975 (ptm160) REVERT: B 296 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8316 (mt) REVERT: B 631 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8242 (mp) REVERT: B 645 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7353 (mtm) REVERT: B 677 TRP cc_start: 0.8053 (OUTLIER) cc_final: 0.7134 (p-90) REVERT: C 77 ARG cc_start: 0.7271 (ttm170) cc_final: 0.7015 (ttp80) REVERT: C 243 ASP cc_start: 0.8528 (p0) cc_final: 0.8010 (p0) REVERT: C 277 MET cc_start: 0.8449 (ttm) cc_final: 0.8149 (ttp) REVERT: C 280 ARG cc_start: 0.7787 (ptp90) cc_final: 0.6994 (ptm160) REVERT: C 296 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8323 (mt) REVERT: C 433 MET cc_start: 0.6940 (mmm) cc_final: 0.6733 (tpp) REVERT: C 631 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8235 (mp) REVERT: C 645 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7338 (mtt) REVERT: C 677 TRP cc_start: 0.8066 (OUTLIER) cc_final: 0.7124 (p-90) REVERT: D 77 ARG cc_start: 0.7265 (ttm170) cc_final: 0.6970 (ttp80) REVERT: D 80 LEU cc_start: 0.8779 (tp) cc_final: 0.8508 (mt) REVERT: D 243 ASP cc_start: 0.8522 (p0) cc_final: 0.8011 (p0) REVERT: D 277 MET cc_start: 0.8481 (ttm) cc_final: 0.8226 (ttp) REVERT: D 280 ARG cc_start: 0.7729 (ptp90) cc_final: 0.6944 (ptm160) REVERT: D 433 MET cc_start: 0.6925 (mmm) cc_final: 0.6723 (tpp) REVERT: D 631 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8264 (mp) REVERT: D 645 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7297 (mtm) REVERT: D 677 TRP cc_start: 0.8046 (OUTLIER) cc_final: 0.7108 (p-90) outliers start: 76 outliers final: 56 residues processed: 331 average time/residue: 0.1370 time to fit residues: 72.6329 Evaluate side-chains 349 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 278 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 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 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 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 296 LEU 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 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 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 296 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 33 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.156447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.135764 restraints weight = 24935.172| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.57 r_work: 0.3511 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19788 Z= 0.155 Angle : 0.553 9.006 26868 Z= 0.278 Chirality : 0.038 0.156 3060 Planarity : 0.004 0.051 3324 Dihedral : 7.416 87.385 2692 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.99 % Allowed : 19.49 % 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 aren not related in a simple way. whole: 1.15 (0.17), residues: 2384 helix: 2.02 (0.14), residues: 1396 sheet: -0.63 (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 C 193 TYR 0.018 0.002 TYR A 447 PHE 0.015 0.001 PHE D 311 TRP 0.014 0.001 TRP A 677 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00369 (19788) covalent geometry : angle 0.55297 (26868) hydrogen bonds : bond 0.03722 ( 1080) hydrogen bonds : angle 3.73492 ( 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 365 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 284 time to evaluate : 0.892 Fit side-chains REVERT: A 75 PHE cc_start: 0.5587 (OUTLIER) cc_final: 0.5016 (t80) REVERT: A 243 ASP cc_start: 0.8602 (p0) cc_final: 0.8008 (p0) REVERT: A 277 MET cc_start: 0.8514 (ttm) cc_final: 0.8214 (ttp) REVERT: A 280 ARG cc_start: 0.7832 (ptp90) cc_final: 0.7000 (ptm160) REVERT: A 412 TYR cc_start: 0.7489 (t80) cc_final: 0.7189 (t80) REVERT: A 631 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8286 (mp) REVERT: A 645 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7332 (mtm) REVERT: A 677 TRP cc_start: 0.8074 (OUTLIER) cc_final: 0.7168 (p-90) REVERT: B 77 ARG cc_start: 0.7289 (ttm170) cc_final: 0.7027 (ttp80) REVERT: B 243 ASP cc_start: 0.8638 (p0) cc_final: 0.8058 (p0) REVERT: B 277 MET cc_start: 0.8501 (ttm) cc_final: 0.8182 (ttp) REVERT: B 280 ARG cc_start: 0.7784 (ptp90) cc_final: 0.6976 (ptm160) REVERT: B 296 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8400 (mt) REVERT: B 631 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 645 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7338 (mtm) REVERT: B 677 TRP cc_start: 0.8100 (OUTLIER) cc_final: 0.7126 (p-90) REVERT: C 77 ARG cc_start: 0.7311 (ttm170) cc_final: 0.7088 (ttp80) REVERT: C 243 ASP cc_start: 0.8612 (p0) cc_final: 0.8113 (p0) REVERT: C 277 MET cc_start: 0.8500 (ttm) cc_final: 0.8182 (ttp) REVERT: C 280 ARG cc_start: 0.7816 (ptp90) cc_final: 0.6988 (ptm160) REVERT: C 296 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8396 (mt) REVERT: C 631 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8254 (mp) REVERT: C 645 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7343 (mtt) REVERT: C 677 TRP cc_start: 0.8103 (OUTLIER) cc_final: 0.7118 (p-90) REVERT: D 77 ARG cc_start: 0.7290 (ttm170) cc_final: 0.7029 (ttp80) REVERT: D 243 ASP cc_start: 0.8618 (p0) cc_final: 0.8044 (p0) REVERT: D 277 MET cc_start: 0.8527 (ttm) cc_final: 0.8212 (ttp) REVERT: D 280 ARG cc_start: 0.7775 (ptp90) cc_final: 0.6978 (ptm160) REVERT: D 631 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8265 (mp) REVERT: D 645 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7315 (mtm) REVERT: D 677 TRP cc_start: 0.8105 (OUTLIER) cc_final: 0.7130 (p-90) outliers start: 81 outliers final: 65 residues processed: 335 average time/residue: 0.1382 time to fit residues: 73.9247 Evaluate side-chains 353 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 273 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 546 VAL 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 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 296 LEU 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 404 MET 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 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 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 296 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 359 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 404 MET 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 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 404 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 52 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 214 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 229 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.159490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.139118 restraints weight = 24817.476| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.55 r_work: 0.3553 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19788 Z= 0.106 Angle : 0.508 8.847 26868 Z= 0.256 Chirality : 0.037 0.153 3060 Planarity : 0.004 0.053 3324 Dihedral : 7.232 89.298 2692 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.89 % Allowed : 19.64 % Favored : 76.48 % 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 aren not related in a simple way. whole: 1.43 (0.17), residues: 2384 helix: 2.28 (0.14), residues: 1396 sheet: -0.57 (0.54), residues: 112 loop : -1.12 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 193 TYR 0.018 0.001 TYR A 447 PHE 0.010 0.001 PHE D 311 TRP 0.011 0.001 TRP A 677 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00238 (19788) covalent geometry : angle 0.50760 (26868) hydrogen bonds : bond 0.03301 ( 1080) hydrogen bonds : angle 3.64400 ( 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 365 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 286 time to evaluate : 0.794 Fit side-chains REVERT: A 75 PHE cc_start: 0.5282 (OUTLIER) cc_final: 0.4444 (t80) REVERT: A 81 PHE cc_start: 0.6767 (m-80) cc_final: 0.6565 (m-80) REVERT: A 243 ASP cc_start: 0.8497 (p0) cc_final: 0.7996 (p0) REVERT: A 277 MET cc_start: 0.8412 (ttm) cc_final: 0.8163 (ttp) REVERT: A 280 ARG cc_start: 0.7795 (ptp90) cc_final: 0.6999 (ptm160) REVERT: A 296 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8341 (mt) REVERT: A 412 TYR cc_start: 0.7321 (t80) cc_final: 0.7003 (t80) REVERT: A 631 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8259 (mp) REVERT: A 645 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7331 (mtm) REVERT: A 677 TRP cc_start: 0.8030 (OUTLIER) cc_final: 0.7068 (p-90) REVERT: B 75 PHE cc_start: 0.5567 (OUTLIER) cc_final: 0.5119 (t80) REVERT: B 80 LEU cc_start: 0.8439 (mt) cc_final: 0.8130 (tp) REVERT: B 243 ASP cc_start: 0.8516 (p0) cc_final: 0.8016 (p0) REVERT: B 277 MET cc_start: 0.8385 (ttm) cc_final: 0.8126 (ttp) REVERT: B 280 ARG cc_start: 0.7766 (ptp90) cc_final: 0.6976 (ptm160) REVERT: B 296 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8307 (mt) REVERT: B 631 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8242 (mp) REVERT: B 645 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7333 (mtt) REVERT: B 677 TRP cc_start: 0.8069 (OUTLIER) cc_final: 0.7138 (p-90) REVERT: C 77 ARG cc_start: 0.7307 (ttm170) cc_final: 0.7030 (ttp80) REVERT: C 243 ASP cc_start: 0.8509 (p0) cc_final: 0.8009 (p0) REVERT: C 277 MET cc_start: 0.8387 (ttm) cc_final: 0.8089 (ttp) REVERT: C 280 ARG cc_start: 0.7782 (ptp90) cc_final: 0.6990 (ptm160) REVERT: C 296 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8311 (mt) REVERT: C 631 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8246 (mp) REVERT: C 645 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7364 (mtt) REVERT: C 677 TRP cc_start: 0.8064 (OUTLIER) cc_final: 0.7133 (p-90) REVERT: D 75 PHE cc_start: 0.5647 (OUTLIER) cc_final: 0.4747 (t80) REVERT: D 243 ASP cc_start: 0.8491 (p0) cc_final: 0.8005 (p0) REVERT: D 277 MET cc_start: 0.8431 (ttm) cc_final: 0.8128 (ttp) REVERT: D 280 ARG cc_start: 0.7767 (ptp90) cc_final: 0.6974 (ptm160) REVERT: D 631 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8266 (mp) REVERT: D 645 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7285 (mtt) REVERT: D 677 TRP cc_start: 0.8075 (OUTLIER) cc_final: 0.7156 (p-90) outliers start: 79 outliers final: 56 residues processed: 338 average time/residue: 0.1371 time to fit residues: 74.6298 Evaluate side-chains 356 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 282 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain A residue 340 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 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 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 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 296 LEU 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 404 MET 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 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 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 296 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 359 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 404 MET 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 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 404 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 231 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 226 optimal weight: 0.0050 chunk 151 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.0010 chunk 228 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 191 HIS ** 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** D 222 GLN ** 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 = 0.3925 r_free = 0.3925 target = 0.161928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142247 restraints weight = 24758.718| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.44 r_work: 0.3583 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19788 Z= 0.094 Angle : 0.485 8.579 26868 Z= 0.244 Chirality : 0.036 0.146 3060 Planarity : 0.004 0.053 3324 Dihedral : 6.982 88.750 2690 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.30 % Allowed : 20.37 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.18), residues: 2384 helix: 2.48 (0.14), residues: 1400 sheet: -0.59 (0.52), residues: 112 loop : -1.08 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 193 TYR 0.018 0.001 TYR A 447 PHE 0.009 0.001 PHE A 311 TRP 0.009 0.001 TRP B 677 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00205 (19788) covalent geometry : angle 0.48508 (26868) hydrogen bonds : bond 0.03031 ( 1080) hydrogen bonds : angle 3.58165 ( 3204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4259.36 seconds wall clock time: 73 minutes 59.21 seconds (4439.21 seconds total)