Starting phenix.real_space_refine on Tue Aug 26 14:39:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jkm_36373/08_2025/8jkm_36373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jkm_36373/08_2025/8jkm_36373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jkm_36373/08_2025/8jkm_36373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jkm_36373/08_2025/8jkm_36373.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jkm_36373/08_2025/8jkm_36373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jkm_36373/08_2025/8jkm_36373.map" } resolution = 3.98 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= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 12316 2.51 5 N 3140 2.21 5 O 3368 1.98 5 H 19252 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38172 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 9543 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 19, 'TRANS': 566} Chain breaks: 4 Restraints were copied for chains: B, C, D Time building chain proxies: 11.33, per 1000 atoms: 0.30 Number of scatterers: 38172 At special positions: 0 Unit cell: (142.29, 142.29, 119.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 3368 8.00 N 3140 7.00 C 12316 6.00 H 19252 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 883.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 68.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.938A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.693A pdb=" N LYS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 215 through 221 removed outlier: 4.199A pdb=" N ARG A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 removed outlier: 4.014A pdb=" N ASN A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 250 through 261 removed outlier: 4.138A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 279 removed outlier: 4.101A pdb=" N GLY A 279 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.827A pdb=" N HIS A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 382 through 391 removed outlier: 4.278A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 452 through 466 Processing helix chain 'A' and resid 466 through 491 Processing helix chain 'A' and resid 504 through 531 Processing helix chain 'A' and resid 550 through 569 Processing helix chain 'A' and resid 575 through 594 removed outlier: 3.767A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 591 " --> pdb=" O MET A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 removed outlier: 4.381A pdb=" N LEU A 598 " --> pdb=" O GLY A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 636 removed outlier: 3.870A pdb=" N LEU A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 631 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 680 removed outlier: 4.420A pdb=" N LEU A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 726 Processing helix chain 'A' and resid 727 through 730 Processing helix chain 'A' and resid 731 through 748 removed outlier: 3.552A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.938A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.693A pdb=" N LYS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 215 through 221 removed outlier: 4.199A pdb=" N ARG B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 removed outlier: 4.014A pdb=" N ASN B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 250 through 261 removed outlier: 4.138A pdb=" N VAL B 254 " --> pdb=" O CYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 275 through 279 removed outlier: 4.101A pdb=" N GLY B 279 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 322 through 331 removed outlier: 3.827A pdb=" N HIS B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 382 through 391 removed outlier: 4.278A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG B 391 " --> pdb=" O GLN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 466 through 491 Processing helix chain 'B' and resid 504 through 531 Processing helix chain 'B' and resid 550 through 569 Processing helix chain 'B' and resid 575 through 594 removed outlier: 3.767A pdb=" N LEU B 590 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 591 " --> pdb=" O MET B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 removed outlier: 4.381A pdb=" N LEU B 598 " --> pdb=" O GLY B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 636 removed outlier: 3.869A pdb=" N LEU B 610 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE B 611 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS B 612 " --> pdb=" O LYS B 608 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 631 " --> pdb=" O GLY B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 680 removed outlier: 4.421A pdb=" N LEU B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 726 Processing helix chain 'B' and resid 727 through 730 Processing helix chain 'B' and resid 731 through 748 removed outlier: 3.552A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.938A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.693A pdb=" N LYS C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 215 through 221 removed outlier: 4.199A pdb=" N ARG C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 removed outlier: 4.014A pdb=" N ASN C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 250 through 261 removed outlier: 4.138A pdb=" N VAL C 254 " --> pdb=" O CYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 279 removed outlier: 4.101A pdb=" N GLY C 279 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 322 through 331 removed outlier: 3.827A pdb=" N HIS C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 357 Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 382 through 391 removed outlier: 4.278A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 452 through 466 Processing helix chain 'C' and resid 466 through 491 Processing helix chain 'C' and resid 504 through 531 Processing helix chain 'C' and resid 550 through 569 Processing helix chain 'C' and resid 575 through 594 removed outlier: 3.767A pdb=" N LEU C 590 " --> pdb=" O TRP C 586 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR C 591 " --> pdb=" O MET C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 599 removed outlier: 4.381A pdb=" N LEU C 598 " --> pdb=" O GLY C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 636 removed outlier: 3.870A pdb=" N LEU C 610 " --> pdb=" O ILE C 606 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE C 611 " --> pdb=" O GLN C 607 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LYS C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 631 " --> pdb=" O GLY C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 680 removed outlier: 4.420A pdb=" N LEU C 670 " --> pdb=" O PHE C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 726 Processing helix chain 'C' and resid 727 through 730 Processing helix chain 'C' and resid 731 through 748 removed outlier: 3.551A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.938A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.693A pdb=" N LYS D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 215 through 221 removed outlier: 4.199A pdb=" N ARG D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 removed outlier: 4.015A pdb=" N ASN D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 Processing helix chain 'D' and resid 250 through 261 removed outlier: 4.138A pdb=" N VAL D 254 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 275 through 279 removed outlier: 4.101A pdb=" N GLY D 279 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 307 Processing helix chain 'D' and resid 322 through 331 removed outlier: 3.827A pdb=" N HIS D 326 " --> pdb=" O ASN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 357 Processing helix chain 'D' and resid 372 through 380 Processing helix chain 'D' and resid 382 through 391 removed outlier: 4.278A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 445 through 450 Processing helix chain 'D' and resid 452 through 466 Processing helix chain 'D' and resid 466 through 491 Processing helix chain 'D' and resid 504 through 531 Processing helix chain 'D' and resid 550 through 569 Processing helix chain 'D' and resid 575 through 594 removed outlier: 3.767A pdb=" N LEU D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR D 591 " --> pdb=" O MET D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 599 removed outlier: 4.381A pdb=" N LEU D 598 " --> pdb=" O GLY D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 636 removed outlier: 3.870A pdb=" N LEU D 610 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE D 611 " --> pdb=" O GLN D 607 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS D 612 " --> pdb=" O LYS D 608 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 631 " --> pdb=" O GLY D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 680 removed outlier: 4.420A pdb=" N LEU D 670 " --> pdb=" O PHE D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 726 Processing helix chain 'D' and resid 727 through 730 Processing helix chain 'D' and resid 731 through 748 removed outlier: 3.552A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 410 removed outlier: 3.665A pdb=" N ASP A 408 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER A 416 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA A 410 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 410 removed outlier: 3.666A pdb=" N ASP B 408 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER B 416 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA B 410 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 410 removed outlier: 3.665A pdb=" N ASP C 408 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER C 416 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA C 410 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 410 removed outlier: 3.665A pdb=" N ASP D 408 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER D 416 " --> pdb=" O ASP D 408 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA D 410 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL D 414 " --> pdb=" O ALA D 410 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 3144 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: 7.79 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19220 1.03 - 1.23: 32 1.23 - 1.42: 8116 1.42 - 1.61: 11056 1.61 - 1.81: 160 Bond restraints: 38584 Sorted by residual: bond pdb=" C GLN D 492 " pdb=" N PRO D 493 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.19e-02 7.06e+03 1.50e+00 bond pdb=" C GLN A 492 " pdb=" N PRO A 493 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.19e-02 7.06e+03 1.50e+00 bond pdb=" C GLN C 492 " pdb=" N PRO C 493 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.19e-02 7.06e+03 1.50e+00 bond pdb=" C GLN B 492 " pdb=" N PRO B 493 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.19e-02 7.06e+03 1.50e+00 bond pdb=" CB MET B 680 " pdb=" CG MET B 680 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.27e+00 ... (remaining 38579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.89: 69664 6.89 - 13.78: 0 13.78 - 20.66: 0 20.66 - 27.55: 8 27.55 - 34.44: 28 Bond angle restraints: 69700 Sorted by residual: angle pdb=" CB ASN D 637 " pdb=" CA ASN D 637 " pdb=" HA ASN D 637 " ideal model delta sigma weight residual 109.00 74.56 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB ASN C 637 " pdb=" CA ASN C 637 " pdb=" HA ASN C 637 " ideal model delta sigma weight residual 109.00 74.56 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB ASN B 637 " pdb=" CA ASN B 637 " pdb=" HA ASN B 637 " ideal model delta sigma weight residual 109.00 74.56 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB ASN A 637 " pdb=" CA ASN A 637 " pdb=" HA ASN A 637 " ideal model delta sigma weight residual 109.00 74.56 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C ASN D 637 " pdb=" CA ASN D 637 " pdb=" HA ASN D 637 " ideal model delta sigma weight residual 109.00 75.32 33.68 3.00e+00 1.11e-01 1.26e+02 ... (remaining 69695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 16127 16.57 - 33.14: 1449 33.14 - 49.71: 296 49.71 - 66.29: 164 66.29 - 82.86: 32 Dihedral angle restraints: 18068 sinusoidal: 9720 harmonic: 8348 Sorted by residual: dihedral pdb=" C ASN B 637 " pdb=" N ASN B 637 " pdb=" CA ASN B 637 " pdb=" CB ASN B 637 " ideal model delta harmonic sigma weight residual -122.60 -133.22 10.62 0 2.50e+00 1.60e-01 1.81e+01 dihedral pdb=" C ASN D 637 " pdb=" N ASN D 637 " pdb=" CA ASN D 637 " pdb=" CB ASN D 637 " ideal model delta harmonic sigma weight residual -122.60 -133.19 10.59 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" C ASN A 637 " pdb=" N ASN A 637 " pdb=" CA ASN A 637 " pdb=" CB ASN A 637 " ideal model delta harmonic sigma weight residual -122.60 -133.18 10.58 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 18065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2939 0.085 - 0.169: 81 0.169 - 0.254: 0 0.254 - 0.339: 0 0.339 - 0.423: 4 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CA ASN D 637 " pdb=" N ASN D 637 " pdb=" C ASN D 637 " pdb=" CB ASN D 637 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA ASN B 637 " pdb=" N ASN B 637 " pdb=" C ASN B 637 " pdb=" CB ASN B 637 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA ASN A 637 " pdb=" N ASN A 637 " pdb=" C ASN A 637 " pdb=" CB ASN A 637 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 3021 not shown) Planarity restraints: 5500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 497 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO C 498 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 498 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 498 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 497 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO D 498 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 498 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 498 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 497 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO A 498 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 498 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 498 " 0.039 5.00e-02 4.00e+02 ... (remaining 5497 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1528 2.14 - 2.76: 74459 2.76 - 3.37: 112258 3.37 - 3.99: 133973 3.99 - 4.60: 211479 Nonbonded interactions: 533697 Sorted by model distance: nonbonded pdb=" O LEU C 676 " pdb=" H GLY C 681 " model vdw 1.526 2.450 nonbonded pdb=" O LEU A 676 " pdb=" H GLY A 681 " model vdw 1.526 2.450 nonbonded pdb=" O LEU D 676 " pdb=" H GLY D 681 " model vdw 1.526 2.450 nonbonded pdb=" O LEU B 676 " pdb=" H GLY B 681 " model vdw 1.526 2.450 nonbonded pdb=" OG SER B 416 " pdb="HH11 ARG B 779 " model vdw 1.578 2.450 ... (remaining 533692 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: 0.07 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 group one per residue 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.250 Extract box with map and model: 0.600 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 34.780 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 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 : 0.003 0.034 19332 Z= 0.134 Angle : 0.608 5.991 26180 Z= 0.339 Chirality : 0.039 0.423 3024 Planarity : 0.004 0.072 3248 Dihedral : 13.651 82.858 7044 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.38 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.18 % 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: -0.33 (0.19), residues: 2304 helix: 0.70 (0.14), residues: 1364 sheet: -1.63 (0.66), residues: 56 loop : -1.57 (0.24), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 661 TYR 0.020 0.002 TYR D 303 PHE 0.016 0.001 PHE C 669 TRP 0.023 0.002 TRP D 586 HIS 0.007 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00276 (19332) covalent geometry : angle 0.60814 (26180) hydrogen bonds : bond 0.13653 ( 1088) hydrogen bonds : angle 6.31335 ( 3144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 601 time to evaluate : 0.972 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.1080 (tpt) cc_final: -0.0010 (tpt) REVERT: A 425 ASP cc_start: 0.7265 (m-30) cc_final: 0.6688 (m-30) REVERT: B 223 MET cc_start: 0.1100 (tpt) cc_final: 0.0003 (tpt) REVERT: C 223 MET cc_start: 0.1074 (tpt) cc_final: -0.0025 (tpt) REVERT: C 425 ASP cc_start: 0.7240 (m-30) cc_final: 0.6661 (m-30) REVERT: D 223 MET cc_start: 0.1098 (tpt) cc_final: -0.0004 (tpt) REVERT: D 425 ASP cc_start: 0.7270 (m-30) cc_final: 0.6701 (m-30) outliers start: 0 outliers final: 0 residues processed: 601 average time/residue: 0.3194 time to fit residues: 280.7537 Evaluate side-chains 408 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 239 GLN C 239 GLN D 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.176024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.142751 restraints weight = 141652.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.148350 restraints weight = 73384.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.151974 restraints weight = 47655.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.154296 restraints weight = 35999.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.155699 restraints weight = 30012.217| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19332 Z= 0.236 Angle : 0.676 9.947 26180 Z= 0.369 Chirality : 0.041 0.448 3024 Planarity : 0.006 0.052 3248 Dihedral : 4.828 21.585 2576 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.29 % Favored : 91.54 % Rotamer: Outliers : 2.07 % Allowed : 11.37 % Favored : 86.56 % 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: -0.92 (0.18), residues: 2304 helix: 0.27 (0.13), residues: 1404 sheet: -2.30 (0.59), residues: 56 loop : -1.96 (0.24), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 661 TYR 0.016 0.002 TYR B 235 PHE 0.027 0.002 PHE B 172 TRP 0.018 0.003 TRP C 586 HIS 0.008 0.002 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00488 (19332) covalent geometry : angle 0.67647 (26180) hydrogen bonds : bond 0.05024 ( 1088) hydrogen bonds : angle 5.53211 ( 3144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 402 time to evaluate : 0.772 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: A 223 MET cc_start: 0.2174 (tpt) cc_final: 0.1431 (tpt) REVERT: A 713 MET cc_start: 0.7094 (tpt) cc_final: 0.6878 (tpt) REVERT: B 223 MET cc_start: 0.2184 (tpt) cc_final: 0.1439 (tpt) REVERT: B 625 MET cc_start: 0.7500 (mtp) cc_final: 0.6863 (mtp) REVERT: C 223 MET cc_start: 0.2154 (tpt) cc_final: 0.1416 (tpt) REVERT: C 625 MET cc_start: 0.7459 (mtp) cc_final: 0.6812 (mtp) REVERT: C 713 MET cc_start: 0.7081 (tpt) cc_final: 0.6868 (tpt) REVERT: D 223 MET cc_start: 0.2165 (tpt) cc_final: 0.1418 (tpt) REVERT: D 553 TYR cc_start: 0.7633 (t80) cc_final: 0.7172 (t80) REVERT: D 625 MET cc_start: 0.7505 (mtp) cc_final: 0.6842 (mtp) REVERT: D 713 MET cc_start: 0.7090 (tpt) cc_final: 0.6883 (tpt) outliers start: 43 outliers final: 27 residues processed: 424 average time/residue: 0.2745 time to fit residues: 180.6472 Evaluate side-chains 392 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 365 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 760 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 145 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.181339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.149847 restraints weight = 137362.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.155684 restraints weight = 69880.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.159436 restraints weight = 44476.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.161770 restraints weight = 32846.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.163307 restraints weight = 27043.347| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19332 Z= 0.122 Angle : 0.589 10.488 26180 Z= 0.308 Chirality : 0.039 0.452 3024 Planarity : 0.004 0.041 3248 Dihedral : 4.334 20.278 2576 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.42 % Favored : 93.40 % Rotamer: Outliers : 1.30 % Allowed : 14.11 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.53 (0.18), residues: 2304 helix: 0.63 (0.13), residues: 1440 sheet: -2.18 (0.59), residues: 56 loop : -2.00 (0.25), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 320 TYR 0.016 0.001 TYR C 303 PHE 0.019 0.001 PHE C 172 TRP 0.016 0.001 TRP D 586 HIS 0.005 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00258 (19332) covalent geometry : angle 0.58858 (26180) hydrogen bonds : bond 0.04119 ( 1088) hydrogen bonds : angle 5.00683 ( 3144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 386 time to evaluate : 0.861 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: A 223 MET cc_start: 0.1829 (tpt) cc_final: 0.1441 (tpt) REVERT: A 425 ASP cc_start: 0.6516 (m-30) cc_final: 0.5545 (m-30) REVERT: B 223 MET cc_start: 0.1723 (tpt) cc_final: 0.1327 (tpt) REVERT: B 425 ASP cc_start: 0.6509 (m-30) cc_final: 0.5534 (m-30) REVERT: B 442 LYS cc_start: 0.7735 (mmtm) cc_final: 0.7203 (mttm) REVERT: B 625 MET cc_start: 0.7420 (mtp) cc_final: 0.6771 (mtp) REVERT: C 223 MET cc_start: 0.1818 (tpt) cc_final: 0.1430 (tpt) REVERT: C 425 ASP cc_start: 0.6512 (m-30) cc_final: 0.5554 (m-30) REVERT: C 442 LYS cc_start: 0.7714 (mmtm) cc_final: 0.7195 (mttm) REVERT: C 625 MET cc_start: 0.7448 (mtp) cc_final: 0.6789 (mtp) REVERT: D 223 MET cc_start: 0.1699 (tpt) cc_final: 0.1309 (tpt) REVERT: D 425 ASP cc_start: 0.6507 (m-30) cc_final: 0.5561 (m-30) REVERT: D 442 LYS cc_start: 0.7711 (mmtm) cc_final: 0.7191 (mttm) REVERT: D 625 MET cc_start: 0.7445 (mtp) cc_final: 0.6773 (mtp) REVERT: D 713 MET cc_start: 0.6872 (tpt) cc_final: 0.6669 (tpt) outliers start: 27 outliers final: 24 residues processed: 402 average time/residue: 0.2847 time to fit residues: 176.5925 Evaluate side-chains 397 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 373 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 685 MET Chi-restraints excluded: chain D residue 697 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 148 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 83 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 120 optimal weight: 0.0000 chunk 229 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN C 474 ASN D 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.179623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.147841 restraints weight = 137661.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.153601 restraints weight = 69687.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.157266 restraints weight = 44287.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.159615 restraints weight = 32890.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.161103 restraints weight = 26991.936| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19332 Z= 0.131 Angle : 0.576 10.622 26180 Z= 0.300 Chirality : 0.039 0.456 3024 Planarity : 0.004 0.038 3248 Dihedral : 4.171 17.375 2576 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.77 % Favored : 94.05 % Rotamer: Outliers : 1.93 % Allowed : 15.56 % Favored : 82.51 % 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: -0.26 (0.18), residues: 2304 helix: 0.87 (0.13), residues: 1432 sheet: -2.10 (0.61), residues: 56 loop : -1.93 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 400 TYR 0.017 0.001 TYR D 556 PHE 0.014 0.001 PHE D 172 TRP 0.014 0.002 TRP B 586 HIS 0.006 0.001 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00278 (19332) covalent geometry : angle 0.57558 (26180) hydrogen bonds : bond 0.03824 ( 1088) hydrogen bonds : angle 4.80017 ( 3144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 398 time to evaluate : 1.011 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.2378 (tpt) cc_final: 0.1637 (tpt) REVERT: A 425 ASP cc_start: 0.6734 (m-30) cc_final: 0.5713 (m-30) REVERT: B 223 MET cc_start: 0.2483 (tpt) cc_final: 0.1722 (tpt) REVERT: B 425 ASP cc_start: 0.6671 (m-30) cc_final: 0.5668 (m-30) REVERT: B 442 LYS cc_start: 0.7692 (mmtm) cc_final: 0.7226 (mttm) REVERT: B 625 MET cc_start: 0.7541 (mtp) cc_final: 0.6934 (mtp) REVERT: B 698 LEU cc_start: 0.8880 (pt) cc_final: 0.8679 (pt) REVERT: C 223 MET cc_start: 0.2461 (tpt) cc_final: 0.1708 (tpt) REVERT: C 425 ASP cc_start: 0.6727 (m-30) cc_final: 0.5726 (m-30) REVERT: C 442 LYS cc_start: 0.7671 (mmtm) cc_final: 0.7218 (mttm) REVERT: C 625 MET cc_start: 0.7521 (mtp) cc_final: 0.6951 (mtp) REVERT: D 223 MET cc_start: 0.2347 (tpt) cc_final: 0.1601 (tpt) REVERT: D 425 ASP cc_start: 0.6735 (m-30) cc_final: 0.5734 (m-30) REVERT: D 442 LYS cc_start: 0.7664 (mmtm) cc_final: 0.7209 (mttm) REVERT: D 482 MET cc_start: 0.8582 (tpp) cc_final: 0.8126 (tpp) REVERT: D 625 MET cc_start: 0.7523 (mtp) cc_final: 0.6941 (mtp) outliers start: 40 outliers final: 37 residues processed: 422 average time/residue: 0.3003 time to fit residues: 194.4686 Evaluate side-chains 416 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 379 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 685 MET Chi-restraints excluded: chain D residue 697 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 53 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 163 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** 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 = 0.4273 r_free = 0.4273 target = 0.167492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.133505 restraints weight = 142819.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.139039 restraints weight = 73823.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.142641 restraints weight = 48222.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.144879 restraints weight = 36646.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.146292 restraints weight = 30752.969| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 19332 Z= 0.318 Angle : 0.798 12.614 26180 Z= 0.432 Chirality : 0.045 0.489 3024 Planarity : 0.006 0.051 3248 Dihedral : 5.311 24.149 2576 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.55 % Favored : 90.28 % Rotamer: Outliers : 3.81 % Allowed : 16.28 % Favored : 79.91 % 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: -1.71 (0.17), residues: 2304 helix: -0.35 (0.13), residues: 1412 sheet: -2.82 (0.56), residues: 56 loop : -2.29 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 400 TYR 0.031 0.003 TYR A 346 PHE 0.021 0.002 PHE C 751 TRP 0.028 0.003 TRP C 586 HIS 0.009 0.002 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00657 (19332) covalent geometry : angle 0.79794 (26180) hydrogen bonds : bond 0.05373 ( 1088) hydrogen bonds : angle 5.49313 ( 3144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 396 time to evaluate : 0.759 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 622 LEU cc_start: 0.8202 (tp) cc_final: 0.7633 (tp) REVERT: A 625 MET cc_start: 0.7720 (mtp) cc_final: 0.7402 (mtp) REVERT: B 372 SER cc_start: 0.8318 (t) cc_final: 0.8037 (p) REVERT: B 625 MET cc_start: 0.7638 (mtp) cc_final: 0.7204 (mtp) REVERT: C 622 LEU cc_start: 0.8308 (tp) cc_final: 0.7633 (tp) REVERT: C 625 MET cc_start: 0.7791 (mtp) cc_final: 0.7298 (mtp) REVERT: D 622 LEU cc_start: 0.8341 (tp) cc_final: 0.7665 (tp) REVERT: D 625 MET cc_start: 0.7764 (mtp) cc_final: 0.7257 (mtp) outliers start: 79 outliers final: 70 residues processed: 444 average time/residue: 0.2900 time to fit residues: 194.8691 Evaluate side-chains 435 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 365 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 406 PHE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 591 TYR Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 685 MET Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 67 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 213 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 113 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.172511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.138897 restraints weight = 142493.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.144558 restraints weight = 72999.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.148261 restraints weight = 47455.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.150557 restraints weight = 35981.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.151606 restraints weight = 30101.103| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19332 Z= 0.146 Angle : 0.614 10.562 26180 Z= 0.320 Chirality : 0.039 0.455 3024 Planarity : 0.004 0.043 3248 Dihedral : 4.636 18.730 2576 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.77 % Favored : 93.06 % Rotamer: Outliers : 3.85 % Allowed : 17.82 % Favored : 78.32 % 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: -0.90 (0.17), residues: 2304 helix: 0.33 (0.13), residues: 1428 sheet: -2.80 (0.58), residues: 56 loop : -2.05 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 757 TYR 0.025 0.002 TYR B 702 PHE 0.015 0.001 PHE B 624 TRP 0.018 0.002 TRP C 586 HIS 0.007 0.001 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00307 (19332) covalent geometry : angle 0.61354 (26180) hydrogen bonds : bond 0.04185 ( 1088) hydrogen bonds : angle 4.95450 ( 3144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 401 time to evaluate : 0.848 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: A 372 SER cc_start: 0.8076 (t) cc_final: 0.7783 (p) REVERT: A 453 GLU cc_start: 0.7915 (tp30) cc_final: 0.7668 (tp30) REVERT: A 457 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8496 (mm-30) REVERT: A 578 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6852 (tmm) REVERT: A 622 LEU cc_start: 0.8214 (tp) cc_final: 0.7700 (tp) REVERT: A 625 MET cc_start: 0.7735 (mtp) cc_final: 0.7369 (mtp) REVERT: A 746 ARG cc_start: 0.8086 (ptp-110) cc_final: 0.7800 (ptp-110) REVERT: B 372 SER cc_start: 0.8151 (t) cc_final: 0.7019 (p) REVERT: B 442 LYS cc_start: 0.7834 (mmtm) cc_final: 0.7358 (mttm) REVERT: B 453 GLU cc_start: 0.7925 (tp30) cc_final: 0.7692 (tp30) REVERT: B 578 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6951 (tmm) REVERT: B 625 MET cc_start: 0.7623 (mtp) cc_final: 0.7146 (mtp) REVERT: B 746 ARG cc_start: 0.8129 (ptp-110) cc_final: 0.7866 (ptp-110) REVERT: C 372 SER cc_start: 0.8089 (t) cc_final: 0.7799 (p) REVERT: C 442 LYS cc_start: 0.7830 (mmtm) cc_final: 0.7349 (mttm) REVERT: C 453 GLU cc_start: 0.7971 (tp30) cc_final: 0.7722 (tp30) REVERT: C 578 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6969 (tmm) REVERT: C 607 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7444 (mm-40) REVERT: C 625 MET cc_start: 0.7726 (mtp) cc_final: 0.7184 (mtp) REVERT: C 746 ARG cc_start: 0.8076 (ptp-110) cc_final: 0.7806 (ptp-110) REVERT: D 372 SER cc_start: 0.8099 (t) cc_final: 0.7799 (p) REVERT: D 442 LYS cc_start: 0.7838 (mmtm) cc_final: 0.7359 (mttm) REVERT: D 453 GLU cc_start: 0.7972 (tp30) cc_final: 0.7725 (tp30) REVERT: D 457 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8511 (mm-30) REVERT: D 625 MET cc_start: 0.7721 (mtp) cc_final: 0.7141 (mtp) REVERT: D 746 ARG cc_start: 0.8139 (ptp-110) cc_final: 0.7891 (ptp-110) outliers start: 80 outliers final: 58 residues processed: 445 average time/residue: 0.2832 time to fit residues: 191.2154 Evaluate side-chains 438 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 376 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 685 MET Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 197 optimal weight: 4.9990 chunk 196 optimal weight: 0.8980 chunk 192 optimal weight: 0.7980 chunk 58 optimal weight: 40.0000 chunk 182 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 101 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.174200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.140966 restraints weight = 142600.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.146791 restraints weight = 73304.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.150473 restraints weight = 47458.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.152785 restraints weight = 35817.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.154211 restraints weight = 29896.910| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19332 Z= 0.128 Angle : 0.601 10.731 26180 Z= 0.308 Chirality : 0.039 0.457 3024 Planarity : 0.004 0.041 3248 Dihedral : 4.358 18.056 2576 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.32 % Rotamer: Outliers : 3.76 % Allowed : 18.88 % 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: -0.42 (0.18), residues: 2304 helix: 0.76 (0.13), residues: 1416 sheet: -2.68 (0.60), residues: 56 loop : -1.92 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 400 TYR 0.016 0.002 TYR C 303 PHE 0.017 0.001 PHE C 524 TRP 0.017 0.002 TRP C 586 HIS 0.008 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00270 (19332) covalent geometry : angle 0.60109 (26180) hydrogen bonds : bond 0.03905 ( 1088) hydrogen bonds : angle 4.73829 ( 3144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 388 time to evaluate : 0.991 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.9029 (tp) cc_final: 0.8811 (mp) REVERT: A 442 LYS cc_start: 0.7661 (mmtm) cc_final: 0.7153 (mttm) REVERT: A 453 GLU cc_start: 0.7995 (tp30) cc_final: 0.7714 (tp30) REVERT: A 578 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6771 (tmm) REVERT: A 622 LEU cc_start: 0.8161 (tp) cc_final: 0.7670 (tp) REVERT: A 625 MET cc_start: 0.7782 (mtp) cc_final: 0.7311 (mtp) REVERT: A 746 ARG cc_start: 0.8026 (ptp-110) cc_final: 0.7720 (ptp-110) REVERT: B 372 SER cc_start: 0.8023 (t) cc_final: 0.7566 (p) REVERT: B 442 LYS cc_start: 0.7857 (mmtm) cc_final: 0.7391 (mttm) REVERT: B 578 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6884 (tmm) REVERT: B 625 MET cc_start: 0.7630 (mtp) cc_final: 0.7117 (mtp) REVERT: B 746 ARG cc_start: 0.8006 (ptp-110) cc_final: 0.7714 (ptp-110) REVERT: C 291 LEU cc_start: 0.9017 (tp) cc_final: 0.8801 (mp) REVERT: C 372 SER cc_start: 0.8012 (t) cc_final: 0.7767 (p) REVERT: C 442 LYS cc_start: 0.7829 (mmtm) cc_final: 0.7368 (mttm) REVERT: C 453 GLU cc_start: 0.8084 (tp30) cc_final: 0.7826 (tp30) REVERT: C 578 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6879 (tmm) REVERT: C 625 MET cc_start: 0.7817 (mtp) cc_final: 0.7270 (mtp) REVERT: C 746 ARG cc_start: 0.7999 (ptp-110) cc_final: 0.7720 (ptp-110) REVERT: D 372 SER cc_start: 0.7993 (t) cc_final: 0.7759 (p) REVERT: D 442 LYS cc_start: 0.7822 (mmtm) cc_final: 0.7363 (mttm) REVERT: D 453 GLU cc_start: 0.8019 (tp30) cc_final: 0.7755 (tp30) REVERT: D 625 MET cc_start: 0.7843 (mtp) cc_final: 0.7284 (mtp) REVERT: D 746 ARG cc_start: 0.8011 (ptp-110) cc_final: 0.7722 (ptp-110) outliers start: 78 outliers final: 68 residues processed: 432 average time/residue: 0.2989 time to fit residues: 192.8787 Evaluate side-chains 447 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 376 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 628 TYR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 628 TYR Chi-restraints excluded: chain D residue 685 MET Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 118 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 135 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 223 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.170191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.136203 restraints weight = 142839.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.141890 restraints weight = 74360.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.145538 restraints weight = 48660.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.147812 restraints weight = 37000.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.149176 restraints weight = 31023.629| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19332 Z= 0.223 Angle : 0.663 10.931 26180 Z= 0.352 Chirality : 0.040 0.462 3024 Planarity : 0.005 0.041 3248 Dihedral : 4.766 23.367 2576 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.59 % Favored : 90.32 % Rotamer: Outliers : 4.05 % Allowed : 19.51 % Favored : 76.45 % 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: -0.98 (0.17), residues: 2304 helix: 0.31 (0.13), residues: 1416 sheet: -2.80 (0.61), residues: 56 loop : -2.15 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 400 TYR 0.025 0.002 TYR D 346 PHE 0.015 0.002 PHE B 624 TRP 0.030 0.002 TRP B 586 HIS 0.008 0.002 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00458 (19332) covalent geometry : angle 0.66296 (26180) hydrogen bonds : bond 0.04465 ( 1088) hydrogen bonds : angle 5.02014 ( 3144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 368 time to evaluate : 0.746 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 342 VAL cc_start: 0.8951 (t) cc_final: 0.8733 (p) REVERT: A 442 LYS cc_start: 0.7627 (mmtm) cc_final: 0.7095 (mttm) REVERT: A 574 TYR cc_start: 0.5453 (m-10) cc_final: 0.5183 (m-10) REVERT: A 578 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6983 (tmm) REVERT: A 622 LEU cc_start: 0.8176 (tp) cc_final: 0.7628 (tp) REVERT: A 625 MET cc_start: 0.7825 (mtp) cc_final: 0.7407 (mtp) REVERT: A 746 ARG cc_start: 0.8074 (ptp-110) cc_final: 0.7745 (ptp-110) REVERT: B 342 VAL cc_start: 0.8954 (t) cc_final: 0.8737 (p) REVERT: B 442 LYS cc_start: 0.7825 (mmtm) cc_final: 0.7276 (mttm) REVERT: B 453 GLU cc_start: 0.7938 (tp30) cc_final: 0.7646 (tp30) REVERT: B 578 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7005 (tmm) REVERT: B 622 LEU cc_start: 0.8170 (tp) cc_final: 0.7618 (tp) REVERT: B 625 MET cc_start: 0.7732 (mtp) cc_final: 0.7262 (mtp) REVERT: B 746 ARG cc_start: 0.8054 (ptp-110) cc_final: 0.7769 (ptp-110) REVERT: C 442 LYS cc_start: 0.7790 (mmtm) cc_final: 0.7260 (mttm) REVERT: C 578 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7007 (tmm) REVERT: C 625 MET cc_start: 0.7866 (mtp) cc_final: 0.7443 (mtp) REVERT: C 746 ARG cc_start: 0.8051 (ptp-110) cc_final: 0.7764 (ptp-110) REVERT: D 442 LYS cc_start: 0.7771 (mmtm) cc_final: 0.7237 (mttm) REVERT: D 625 MET cc_start: 0.7841 (mtp) cc_final: 0.7422 (mtp) REVERT: D 746 ARG cc_start: 0.8063 (ptp-110) cc_final: 0.7756 (ptp-110) outliers start: 84 outliers final: 73 residues processed: 415 average time/residue: 0.2963 time to fit residues: 186.1370 Evaluate side-chains 431 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 355 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 553 TYR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 553 TYR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 628 TYR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 628 TYR Chi-restraints excluded: chain D residue 685 MET Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 53 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.171485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.138046 restraints weight = 142627.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.143742 restraints weight = 73157.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.147428 restraints weight = 47522.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.149745 restraints weight = 35875.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.151158 restraints weight = 29941.268| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19332 Z= 0.165 Angle : 0.629 10.747 26180 Z= 0.327 Chirality : 0.039 0.458 3024 Planarity : 0.004 0.042 3248 Dihedral : 4.591 20.867 2576 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.38 % Favored : 91.58 % Rotamer: Outliers : 4.24 % Allowed : 20.62 % Favored : 75.14 % 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: -0.80 (0.17), residues: 2304 helix: 0.51 (0.13), residues: 1412 sheet: -2.75 (0.61), residues: 56 loop : -2.19 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 400 TYR 0.020 0.002 TYR B 346 PHE 0.014 0.001 PHE B 524 TRP 0.028 0.002 TRP B 586 HIS 0.009 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00343 (19332) covalent geometry : angle 0.62855 (26180) hydrogen bonds : bond 0.04163 ( 1088) hydrogen bonds : angle 4.87173 ( 3144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 368 time to evaluate : 1.037 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 342 VAL cc_start: 0.8916 (t) cc_final: 0.8704 (p) REVERT: A 442 LYS cc_start: 0.7640 (mmtm) cc_final: 0.7092 (mttm) REVERT: A 453 GLU cc_start: 0.7995 (tp30) cc_final: 0.7758 (tp30) REVERT: A 464 ARG cc_start: 0.7147 (tpt170) cc_final: 0.6914 (tpt170) REVERT: A 578 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6875 (tmm) REVERT: A 622 LEU cc_start: 0.8195 (tp) cc_final: 0.7638 (tp) REVERT: A 625 MET cc_start: 0.7814 (mtp) cc_final: 0.7358 (mtp) REVERT: A 746 ARG cc_start: 0.8025 (ptp-110) cc_final: 0.7728 (ptp-110) REVERT: B 342 VAL cc_start: 0.8917 (t) cc_final: 0.8706 (p) REVERT: B 442 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7234 (mttm) REVERT: B 464 ARG cc_start: 0.7138 (tpt170) cc_final: 0.6897 (tpt170) REVERT: B 622 LEU cc_start: 0.8177 (tp) cc_final: 0.7638 (tp) REVERT: B 625 MET cc_start: 0.7782 (mtp) cc_final: 0.7339 (mtp) REVERT: B 746 ARG cc_start: 0.8049 (ptp-110) cc_final: 0.7780 (ptp-110) REVERT: C 442 LYS cc_start: 0.7768 (mmtm) cc_final: 0.7225 (mttm) REVERT: C 453 GLU cc_start: 0.7971 (tp30) cc_final: 0.7697 (tp30) REVERT: C 625 MET cc_start: 0.7864 (mtp) cc_final: 0.7429 (mtp) REVERT: C 746 ARG cc_start: 0.8029 (ptp-110) cc_final: 0.7747 (ptp-110) REVERT: D 372 SER cc_start: 0.8001 (t) cc_final: 0.7773 (p) REVERT: D 442 LYS cc_start: 0.7772 (mmtm) cc_final: 0.7230 (mttm) REVERT: D 464 ARG cc_start: 0.7147 (tpt170) cc_final: 0.6905 (tpt170) REVERT: D 625 MET cc_start: 0.7846 (mtp) cc_final: 0.7391 (mtp) REVERT: D 746 ARG cc_start: 0.8039 (ptp-110) cc_final: 0.7762 (ptp-110) outliers start: 88 outliers final: 82 residues processed: 412 average time/residue: 0.2839 time to fit residues: 175.7780 Evaluate side-chains 446 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 363 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 553 TYR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 553 TYR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 605 MET Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 628 TYR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 628 TYR Chi-restraints excluded: chain D residue 685 MET Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 103 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.173448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.139285 restraints weight = 142315.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.145107 restraints weight = 74055.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.148835 restraints weight = 48224.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.151188 restraints weight = 36469.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.152668 restraints weight = 30443.379| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19332 Z= 0.139 Angle : 0.621 10.774 26180 Z= 0.319 Chirality : 0.039 0.457 3024 Planarity : 0.004 0.041 3248 Dihedral : 4.417 18.913 2576 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.29 % Favored : 91.67 % Rotamer: Outliers : 3.76 % Allowed : 21.44 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.18), residues: 2304 helix: 0.76 (0.13), residues: 1408 sheet: -2.68 (0.62), residues: 56 loop : -2.18 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 400 TYR 0.021 0.002 TYR B 702 PHE 0.023 0.001 PHE B 624 TRP 0.028 0.002 TRP B 586 HIS 0.011 0.001 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00296 (19332) covalent geometry : angle 0.62053 (26180) hydrogen bonds : bond 0.03991 ( 1088) hydrogen bonds : angle 4.75716 ( 3144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 373 time to evaluate : 0.807 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: 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 160 ARG cc_start: 0.7450 (mmm160) cc_final: 0.7115 (tmt-80) REVERT: A 342 VAL cc_start: 0.8895 (t) cc_final: 0.8670 (p) REVERT: A 442 LYS cc_start: 0.7609 (mmtm) cc_final: 0.7082 (mttm) REVERT: A 453 GLU cc_start: 0.7990 (tp30) cc_final: 0.7728 (tp30) REVERT: A 464 ARG cc_start: 0.7110 (tpt170) cc_final: 0.6887 (tpt170) REVERT: A 482 MET cc_start: 0.7859 (tpp) cc_final: 0.7415 (tpp) REVERT: A 578 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6840 (tmm) REVERT: A 622 LEU cc_start: 0.8194 (tp) cc_final: 0.7654 (tp) REVERT: A 625 MET cc_start: 0.7855 (mtp) cc_final: 0.7397 (mtp) REVERT: A 746 ARG cc_start: 0.8005 (ptp-110) cc_final: 0.7689 (ptp-110) REVERT: B 160 ARG cc_start: 0.7484 (mmm160) cc_final: 0.7149 (tmt-80) REVERT: B 342 VAL cc_start: 0.8889 (t) cc_final: 0.8669 (p) REVERT: B 442 LYS cc_start: 0.7705 (mmtm) cc_final: 0.7193 (mttm) REVERT: B 464 ARG cc_start: 0.7094 (tpt170) cc_final: 0.6852 (tpt170) REVERT: B 622 LEU cc_start: 0.8170 (tp) cc_final: 0.7691 (tp) REVERT: B 625 MET cc_start: 0.7813 (mtp) cc_final: 0.7325 (mtp) REVERT: B 746 ARG cc_start: 0.8011 (ptp-110) cc_final: 0.7710 (ptp-110) REVERT: C 160 ARG cc_start: 0.7451 (mmm160) cc_final: 0.7111 (tmt-80) REVERT: C 442 LYS cc_start: 0.7714 (mmtm) cc_final: 0.7212 (mttm) REVERT: C 464 ARG cc_start: 0.7086 (tpt170) cc_final: 0.6840 (tpt170) REVERT: C 625 MET cc_start: 0.7849 (mtp) cc_final: 0.7414 (mtp) REVERT: C 746 ARG cc_start: 0.8014 (ptp-110) cc_final: 0.7711 (ptp-110) REVERT: D 160 ARG cc_start: 0.7486 (mmm160) cc_final: 0.7142 (tmt-80) REVERT: D 372 SER cc_start: 0.7987 (t) cc_final: 0.7786 (p) REVERT: D 442 LYS cc_start: 0.7690 (mmtm) cc_final: 0.7198 (mttm) REVERT: D 453 GLU cc_start: 0.8003 (tp30) cc_final: 0.7731 (tp30) REVERT: D 464 ARG cc_start: 0.7116 (tpt170) cc_final: 0.6880 (tpt170) REVERT: D 625 MET cc_start: 0.7844 (mtp) cc_final: 0.7397 (mtp) REVERT: D 746 ARG cc_start: 0.8010 (ptp-110) cc_final: 0.7710 (ptp-110) outliers start: 78 outliers final: 74 residues processed: 413 average time/residue: 0.2806 time to fit residues: 174.9042 Evaluate side-chains 444 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 369 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 553 TYR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 685 MET Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 553 TYR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 628 TYR Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 628 TYR Chi-restraints excluded: chain D residue 685 MET Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 191 optimal weight: 0.0670 chunk 9 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 218 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 239 GLN C 239 GLN D 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.175432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.141734 restraints weight = 140926.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.147552 restraints weight = 73181.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.151282 restraints weight = 47540.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.153648 restraints weight = 35773.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.155121 restraints weight = 29740.604| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19332 Z= 0.118 Angle : 0.602 10.784 26180 Z= 0.308 Chirality : 0.038 0.457 3024 Planarity : 0.004 0.041 3248 Dihedral : 4.199 16.924 2576 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.94 % Favored : 93.01 % Rotamer: Outliers : 3.56 % Allowed : 21.15 % Favored : 75.29 % 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: -0.30 (0.18), residues: 2304 helix: 0.95 (0.13), residues: 1432 sheet: -2.62 (0.63), residues: 56 loop : -2.15 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 400 TYR 0.018 0.001 TYR A 556 PHE 0.017 0.001 PHE C 524 TRP 0.028 0.002 TRP B 586 HIS 0.011 0.001 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00258 (19332) covalent geometry : angle 0.60223 (26180) hydrogen bonds : bond 0.03730 ( 1088) hydrogen bonds : angle 4.57215 ( 3144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6061.61 seconds wall clock time: 104 minutes 6.58 seconds (6246.58 seconds total)