Starting phenix.real_space_refine on Thu Aug 6 01:19:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ioa_35613/08_2026/8ioa_35613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ioa_35613/08_2026/8ioa_35613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ioa_35613/08_2026/8ioa_35613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ioa_35613/08_2026/8ioa_35613.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ioa_35613/08_2026/8ioa_35613.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ioa_35613/08_2026/8ioa_35613.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ioa_35613/08_2026/8ioa_35613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ioa_35613/08_2026/8ioa_35613.map" } resolution = 2.63 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= 0.004 sd= 0.048 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 32 5.16 5 C 7972 2.51 5 N 2252 2.21 5 O 2308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12570 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "B" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.93, per 1000 atoms: 0.31 Number of scatterers: 12570 At special positions: 0 Unit cell: (98.4, 107.42, 99.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 4 15.00 Mg 2 11.99 O 2308 8.00 N 2252 7.00 C 7972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 891.9 milliseconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2932 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 10 sheets defined 51.0% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 63 through 82 removed outlier: 3.566A pdb=" N HIS A 73 " --> pdb=" O PHE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 106 removed outlier: 3.589A pdb=" N LEU A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 118 through 129 removed outlier: 4.018A pdb=" N PHE A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.599A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 247 through 275 removed outlier: 4.230A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 337 through 342 removed outlier: 5.990A pdb=" N GLU A 340 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.939A pdb=" N ILE A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 removed outlier: 3.741A pdb=" N ARG A 363 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N MET A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N SER A 365 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 367 " --> pdb=" O MET A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 401 through 416 removed outlier: 4.236A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 449 through 455 removed outlier: 4.007A pdb=" N GLU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.614A pdb=" N LEU A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 499 through 516 Processing helix chain 'A' and resid 547 through 556 removed outlier: 3.957A pdb=" N ASP A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 580 Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 636 through 653 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 680 through 688 Processing helix chain 'A' and resid 702 through 709 removed outlier: 4.083A pdb=" N HIS A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 716 removed outlier: 3.545A pdb=" N HIS A 715 " --> pdb=" O ARG A 712 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN A 716 " --> pdb=" O HIS A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 712 through 716' Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 755 through 758 removed outlier: 3.739A pdb=" N ARG A 758 " --> pdb=" O PRO A 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 758' Processing helix chain 'A' and resid 761 through 783 Processing helix chain 'A' and resid 786 through 791 Processing helix chain 'B' and resid 14 through 38 Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.509A pdb=" N ILE B 53 " --> pdb=" O PRO B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 82 removed outlier: 3.600A pdb=" N HIS B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 106 removed outlier: 3.561A pdb=" N LEU B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 118 through 129 removed outlier: 4.006A pdb=" N PHE B 129 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 164 Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.633A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 removed outlier: 3.570A pdb=" N LEU B 196 " --> pdb=" O ASN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 247 through 275 removed outlier: 4.231A pdb=" N GLY B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 337 through 342 removed outlier: 5.988A pdb=" N GLU B 340 " --> pdb=" O TYR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.721A pdb=" N ARG B 363 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 401 through 416 removed outlier: 4.297A pdb=" N LEU B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 439 removed outlier: 3.528A pdb=" N VAL B 439 " --> pdb=" O VAL B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 removed outlier: 3.978A pdb=" N GLU B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 454 " --> pdb=" O PRO B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 499 through 516 Processing helix chain 'B' and resid 547 through 556 removed outlier: 3.973A pdb=" N ASP B 551 " --> pdb=" O PRO B 547 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 580 Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 636 through 653 Processing helix chain 'B' and resid 665 through 669 Processing helix chain 'B' and resid 680 through 688 Processing helix chain 'B' and resid 702 through 709 removed outlier: 4.069A pdb=" N HIS B 706 " --> pdb=" O PRO B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 716 removed outlier: 3.542A pdb=" N HIS B 715 " --> pdb=" O ARG B 712 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN B 716 " --> pdb=" O HIS B 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 712 through 716' Processing helix chain 'B' and resid 731 through 739 Processing helix chain 'B' and resid 742 through 754 Processing helix chain 'B' and resid 755 through 758 removed outlier: 3.509A pdb=" N ARG B 758 " --> pdb=" O PRO B 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 758' Processing helix chain 'B' and resid 761 through 783 Processing helix chain 'B' and resid 786 through 791 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 177 removed outlier: 6.492A pdb=" N VAL A 172 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 207 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N CYS A 174 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N HIS A 209 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 176 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 465 removed outlier: 8.381A pdb=" N MET A 465 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 422 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY A 487 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LEU A 529 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE A 489 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER A 531 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 491 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 442 through 443 removed outlier: 5.472A pdb=" N LYS A 442 " --> pdb=" O SER A 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 613 through 615 removed outlier: 6.514A pdb=" N VAL A 630 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASN A 697 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA A 632 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 171 through 177 removed outlier: 6.498A pdb=" N VAL B 172 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE B 207 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N CYS B 174 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS B 209 " --> pdb=" O CYS B 174 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE B 176 " --> pdb=" O HIS B 209 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 397 through 400 removed outlier: 4.708A pdb=" N SER B 397 " --> pdb=" O GLN B 598 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 464 through 465 removed outlier: 8.414A pdb=" N MET B 465 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 422 " --> pdb=" O MET B 465 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY B 487 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LEU B 529 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE B 489 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER B 531 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR B 491 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 442 through 443 removed outlier: 5.545A pdb=" N LYS B 442 " --> pdb=" O SER B 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 613 through 615 removed outlier: 6.551A pdb=" N VAL B 629 " --> pdb=" O ARG B 659 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL B 661 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE B 631 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL B 663 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER B 633 " --> pdb=" O VAL B 663 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 630 " --> pdb=" O ILE B 695 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASN B 697 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 632 " --> pdb=" O ASN B 697 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1516 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: 1.66 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2091 1.30 - 1.43: 3541 1.43 - 1.55: 7246 1.55 - 1.68: 8 1.68 - 1.81: 46 Bond restraints: 12932 Sorted by residual: bond pdb=" C ASN A 697 " pdb=" O ASN A 697 " ideal model delta sigma weight residual 1.235 1.172 0.064 1.22e-02 6.72e+03 2.72e+01 bond pdb=" O1A TPP A 802 " pdb=" PA TPP A 802 " ideal model delta sigma weight residual 1.479 1.524 -0.045 1.00e-02 1.00e+04 2.01e+01 bond pdb=" O1A TPP B 801 " pdb=" PA TPP B 801 " ideal model delta sigma weight residual 1.479 1.523 -0.044 1.00e-02 1.00e+04 1.90e+01 bond pdb=" CA ASN A 697 " pdb=" CB ASN A 697 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.43e-02 4.89e+03 7.76e+00 bond pdb=" CG ASN A 697 " pdb=" OD1 ASN A 697 " ideal model delta sigma weight residual 1.231 1.181 0.050 1.90e-02 2.77e+03 6.93e+00 ... (remaining 12927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 17291 1.42 - 2.85: 250 2.85 - 4.27: 89 4.27 - 5.70: 18 5.70 - 7.12: 8 Bond angle restraints: 17656 Sorted by residual: angle pdb=" N ASN B 621 " pdb=" CA ASN B 621 " pdb=" C ASN B 621 " ideal model delta sigma weight residual 111.14 116.88 -5.74 1.08e+00 8.57e-01 2.83e+01 angle pdb=" O3A TPP A 802 " pdb=" PB TPP A 802 " pdb=" O3B TPP A 802 " ideal model delta sigma weight residual 104.26 111.21 -6.95 1.33e+00 5.64e-01 2.72e+01 angle pdb=" O2B TPP B 801 " pdb=" PB TPP B 801 " pdb=" O3A TPP B 801 " ideal model delta sigma weight residual 104.26 111.04 -6.78 1.33e+00 5.64e-01 2.59e+01 angle pdb=" N LEU B 666 " pdb=" CA LEU B 666 " pdb=" C LEU B 666 " ideal model delta sigma weight residual 111.28 116.13 -4.85 1.09e+00 8.42e-01 1.98e+01 angle pdb=" N ARG B 39 " pdb=" CA ARG B 39 " pdb=" C ARG B 39 " ideal model delta sigma weight residual 114.56 108.93 5.63 1.27e+00 6.20e-01 1.96e+01 ... (remaining 17651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.77: 6935 13.77 - 27.53: 499 27.53 - 41.30: 122 41.30 - 55.06: 25 55.06 - 68.83: 9 Dihedral angle restraints: 7590 sinusoidal: 3032 harmonic: 4558 Sorted by residual: dihedral pdb=" CA TRP B 295 " pdb=" C TRP B 295 " pdb=" N THR B 296 " pdb=" CA THR B 296 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.52e+00 dihedral pdb=" CA GLU B 466 " pdb=" CB GLU B 466 " pdb=" CG GLU B 466 " pdb=" CD GLU B 466 " ideal model delta sinusoidal sigma weight residual -180.00 -120.11 -59.89 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU B 733 " pdb=" CB LEU B 733 " pdb=" CG LEU B 733 " pdb=" CD1 LEU B 733 " ideal model delta sinusoidal sigma weight residual 180.00 121.03 58.97 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 7587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1356 0.041 - 0.082: 367 0.082 - 0.123: 154 0.123 - 0.164: 9 0.164 - 0.204: 2 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CA LYS A 214 " pdb=" N LYS A 214 " pdb=" C LYS A 214 " pdb=" CB LYS A 214 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASN B 621 " pdb=" N ASN B 621 " pdb=" C ASN B 621 " pdb=" CB ASN B 621 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA LEU B 666 " pdb=" N LEU B 666 " pdb=" C LEU B 666 " pdb=" CB LEU B 666 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1885 not shown) Planarity restraints: 2324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 453 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C GLU A 453 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU A 453 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 454 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 696 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C PHE A 696 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE A 696 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 697 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 213 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C TYR A 213 " -0.037 2.00e-02 2.50e+03 pdb=" O TYR A 213 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 214 " 0.012 2.00e-02 2.50e+03 ... (remaining 2321 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 63 2.47 - 3.08: 9046 3.08 - 3.69: 19389 3.69 - 4.29: 30610 4.29 - 4.90: 51276 Nonbonded interactions: 110384 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O3B TPP A 802 " model vdw 1.866 2.170 nonbonded pdb=" O1A TPP B 801 " pdb="MG MG B 802 " model vdw 2.068 2.170 nonbonded pdb=" O1B TPP B 801 " pdb="MG MG B 802 " model vdw 2.097 2.170 nonbonded pdb=" OD1 ASN A 211 " pdb="MG MG A 801 " model vdw 2.102 2.170 nonbonded pdb=" OD1 ASP A 178 " pdb="MG MG A 801 " model vdw 2.123 2.170 ... (remaining 110379 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 702 or resid 704 through 718 or resid 720 throug \ h 796)) selection = (chain 'B' and (resid 9 through 702 or resid 704 through 718 or resid 720 throug \ h 796)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.640 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 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 : 0.005 0.064 12932 Z= 0.230 Angle : 0.517 7.119 17656 Z= 0.278 Chirality : 0.044 0.204 1888 Planarity : 0.004 0.038 2324 Dihedral : 10.643 68.825 4658 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.53 % Allowed : 4.06 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.22), residues: 1576 helix: 1.53 (0.20), residues: 674 sheet: 0.31 (0.41), residues: 188 loop : -0.51 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 338 TYR 0.008 0.001 TYR B 480 PHE 0.010 0.001 PHE B 233 TRP 0.016 0.001 TRP A 295 HIS 0.003 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (12932) covalent geometry : angle 0.51699 / 0.28 (17656) hydrogen bonds : bond 0.22216 / 15.14 ( 547) hydrogen bonds : angle 6.09283 / 4.51 ( 1516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.317 Fit side-chains REVERT: A 474 GLU cc_start: 0.8793 (tp30) cc_final: 0.8538 (tp30) REVERT: A 681 ASP cc_start: 0.8040 (m-30) cc_final: 0.7823 (m-30) REVERT: A 734 GLU cc_start: 0.7949 (tt0) cc_final: 0.7593 (tt0) REVERT: B 474 GLU cc_start: 0.8763 (tp30) cc_final: 0.8321 (tp30) REVERT: B 478 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7692 (mt-10) REVERT: B 500 ASP cc_start: 0.8420 (t0) cc_final: 0.8191 (t0) REVERT: B 681 ASP cc_start: 0.7970 (m-30) cc_final: 0.7739 (m-30) outliers start: 7 outliers final: 2 residues processed: 104 average time/residue: 0.6092 time to fit residues: 68.3785 Evaluate side-chains 62 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 613 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 217 ASN A 544 HIS A 677 HIS A 719 HIS B A 771 GLN B 128 GLN B 313 HIS B 537 GLN B 544 HIS B 771 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.092978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.067729 restraints weight = 34369.546| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.67 r_work: 0.2729 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12932 Z= 0.128 Angle : 0.546 6.861 17656 Z= 0.280 Chirality : 0.044 0.137 1888 Planarity : 0.005 0.044 2324 Dihedral : 4.840 45.146 1742 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.20 % Allowed : 6.62 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1576 helix: 1.66 (0.20), residues: 700 sheet: 0.18 (0.41), residues: 172 loop : -0.29 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 758 TYR 0.013 0.001 TYR A 108 PHE 0.011 0.001 PHE B 495 TRP 0.012 0.001 TRP B 295 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (12932) covalent geometry : angle 0.54570 / 0.28 (17656) hydrogen bonds : bond 0.04067 / 2.90 ( 547) hydrogen bonds : angle 4.39407 / 3.25 ( 1516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.393 Fit side-chains REVERT: A 674 GLU cc_start: 0.8217 (mp0) cc_final: 0.7975 (mp0) REVERT: A 721 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7982 (mmp-170) REVERT: A 749 ASP cc_start: 0.8042 (m-30) cc_final: 0.7821 (m-30) REVERT: A 791 GLN cc_start: 0.8939 (mm110) cc_final: 0.8722 (mt0) REVERT: B 474 GLU cc_start: 0.8880 (tp30) cc_final: 0.8334 (tp30) REVERT: B 681 ASP cc_start: 0.8176 (m-30) cc_final: 0.7954 (m-30) REVERT: B 721 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8267 (mmp-170) REVERT: B 734 GLU cc_start: 0.8347 (tt0) cc_final: 0.8061 (tt0) REVERT: B 749 ASP cc_start: 0.8122 (m-30) cc_final: 0.7818 (m-30) outliers start: 16 outliers final: 3 residues processed: 92 average time/residue: 0.5692 time to fit residues: 57.4411 Evaluate side-chains 68 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 721 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 47 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 122 optimal weight: 0.0070 chunk 30 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 677 HIS ** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.093711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.067260 restraints weight = 52717.899| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 4.41 r_work: 0.2714 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12932 Z= 0.114 Angle : 0.502 5.976 17656 Z= 0.255 Chirality : 0.042 0.144 1888 Planarity : 0.004 0.046 2324 Dihedral : 4.689 56.604 1738 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.05 % Allowed : 7.44 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.22), residues: 1576 helix: 1.87 (0.20), residues: 688 sheet: 0.09 (0.40), residues: 174 loop : -0.24 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 738 TYR 0.010 0.001 TYR B 492 PHE 0.013 0.001 PHE B 495 TRP 0.012 0.001 TRP B 295 HIS 0.010 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (12932) covalent geometry : angle 0.50243 / 0.25 (17656) hydrogen bonds : bond 0.03468 / 2.45 ( 547) hydrogen bonds : angle 4.03964 / 2.98 ( 1516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.494 Fit side-chains REVERT: A 721 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7913 (mmp-170) REVERT: A 734 GLU cc_start: 0.8607 (tt0) cc_final: 0.8313 (tt0) REVERT: A 738 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.8380 (ttm-80) REVERT: A 749 ASP cc_start: 0.8071 (m-30) cc_final: 0.7767 (m-30) REVERT: B 277 GLU cc_start: 0.8274 (pp20) cc_final: 0.8002 (pp20) REVERT: B 734 GLU cc_start: 0.8504 (tt0) cc_final: 0.8261 (tt0) REVERT: B 738 ARG cc_start: 0.8581 (mmp80) cc_final: 0.8245 (ttm-80) outliers start: 14 outliers final: 5 residues processed: 95 average time/residue: 0.5314 time to fit residues: 55.9298 Evaluate side-chains 72 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN A 677 HIS B 677 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.068915 restraints weight = 38715.276| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.82 r_work: 0.2758 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12932 Z= 0.114 Angle : 0.500 5.549 17656 Z= 0.253 Chirality : 0.042 0.145 1888 Planarity : 0.004 0.049 2324 Dihedral : 4.661 56.161 1738 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.50 % Allowed : 7.44 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.22), residues: 1576 helix: 1.93 (0.20), residues: 688 sheet: 0.10 (0.40), residues: 174 loop : -0.18 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 515 TYR 0.011 0.001 TYR A 492 PHE 0.010 0.001 PHE B 495 TRP 0.012 0.001 TRP B 295 HIS 0.008 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (12932) covalent geometry : angle 0.50042 / 0.25 (17656) hydrogen bonds : bond 0.03156 / 2.23 ( 547) hydrogen bonds : angle 3.92607 / 2.88 ( 1516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.479 Fit side-chains REVERT: A 516 GLU cc_start: 0.8316 (mp0) cc_final: 0.8032 (mp0) REVERT: A 537 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: A 674 GLU cc_start: 0.8226 (mp0) cc_final: 0.7952 (mp0) REVERT: A 721 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7834 (mmp-170) REVERT: A 734 GLU cc_start: 0.8502 (tt0) cc_final: 0.8237 (tt0) REVERT: A 749 ASP cc_start: 0.8014 (m-30) cc_final: 0.7687 (m-30) REVERT: B 277 GLU cc_start: 0.8272 (pp20) cc_final: 0.8006 (pp20) REVERT: B 721 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8247 (mmp-170) REVERT: B 734 GLU cc_start: 0.8458 (tt0) cc_final: 0.8220 (tt0) REVERT: B 738 ARG cc_start: 0.8700 (mmp80) cc_final: 0.8339 (ttm-80) REVERT: B 791 GLN cc_start: 0.8882 (mt0) cc_final: 0.8610 (mm-40) outliers start: 20 outliers final: 7 residues processed: 86 average time/residue: 0.5096 time to fit residues: 48.5403 Evaluate side-chains 77 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 721 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 138 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 HIS A 771 GLN B 677 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.093370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.067296 restraints weight = 44795.126| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 4.11 r_work: 0.2715 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12932 Z= 0.147 Angle : 0.505 5.496 17656 Z= 0.257 Chirality : 0.044 0.247 1888 Planarity : 0.004 0.051 2324 Dihedral : 4.641 49.218 1738 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.50 % Allowed : 7.74 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.22), residues: 1576 helix: 1.95 (0.20), residues: 688 sheet: 0.08 (0.40), residues: 174 loop : -0.19 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 758 TYR 0.008 0.001 TYR B 492 PHE 0.009 0.001 PHE B 125 TRP 0.011 0.001 TRP B 295 HIS 0.006 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (12932) covalent geometry : angle 0.50532 / 0.26 (17656) hydrogen bonds : bond 0.03281 / 2.33 ( 547) hydrogen bonds : angle 3.88403 / 2.85 ( 1516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.351 Fit side-chains REVERT: A 674 GLU cc_start: 0.8184 (mp0) cc_final: 0.7971 (mp0) REVERT: A 721 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7836 (mmp-170) REVERT: A 734 GLU cc_start: 0.8501 (tt0) cc_final: 0.8174 (tt0) REVERT: A 738 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8330 (ttm-80) REVERT: A 749 ASP cc_start: 0.8013 (m-30) cc_final: 0.7685 (m-30) REVERT: B 277 GLU cc_start: 0.8291 (pp20) cc_final: 0.8063 (pp20) REVERT: B 474 GLU cc_start: 0.8982 (tp30) cc_final: 0.8519 (tp30) REVERT: B 552 LEU cc_start: 0.8501 (tt) cc_final: 0.8289 (tp) REVERT: B 721 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8278 (mmp-170) REVERT: B 734 GLU cc_start: 0.8419 (tt0) cc_final: 0.8172 (tt0) REVERT: B 738 ARG cc_start: 0.8725 (mmp80) cc_final: 0.8361 (ttm-80) outliers start: 20 outliers final: 8 residues processed: 83 average time/residue: 0.5262 time to fit residues: 47.9504 Evaluate side-chains 73 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 746 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 97 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 59 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 HIS B 677 HIS B 771 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.092747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.067896 restraints weight = 37957.690| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.73 r_work: 0.2702 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12932 Z= 0.144 Angle : 0.505 5.683 17656 Z= 0.257 Chirality : 0.044 0.212 1888 Planarity : 0.004 0.056 2324 Dihedral : 4.634 53.215 1738 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.13 % Allowed : 8.27 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.22), residues: 1576 helix: 1.97 (0.20), residues: 688 sheet: 0.14 (0.40), residues: 170 loop : -0.18 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 758 TYR 0.009 0.001 TYR B 492 PHE 0.009 0.001 PHE B 495 TRP 0.012 0.001 TRP B 295 HIS 0.006 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (12932) covalent geometry : angle 0.50544 / 0.26 (17656) hydrogen bonds : bond 0.03233 / 2.29 ( 547) hydrogen bonds : angle 3.83204 / 2.81 ( 1516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.360 Fit side-chains REVERT: A 537 GLN cc_start: 0.8657 (tt0) cc_final: 0.7998 (pp30) REVERT: A 674 GLU cc_start: 0.8143 (mp0) cc_final: 0.7892 (mp0) REVERT: A 721 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7805 (mmp-170) REVERT: A 734 GLU cc_start: 0.8490 (tt0) cc_final: 0.8271 (tt0) REVERT: A 749 ASP cc_start: 0.7997 (m-30) cc_final: 0.7668 (m-30) REVERT: B 277 GLU cc_start: 0.8263 (pp20) cc_final: 0.7997 (pp20) REVERT: B 474 GLU cc_start: 0.8985 (tp30) cc_final: 0.8516 (tp30) REVERT: B 721 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8313 (mmp-170) REVERT: B 734 GLU cc_start: 0.8410 (tt0) cc_final: 0.8141 (tt0) REVERT: B 738 ARG cc_start: 0.8761 (mmp80) cc_final: 0.8400 (ttm-80) outliers start: 15 outliers final: 9 residues processed: 84 average time/residue: 0.4933 time to fit residues: 45.8730 Evaluate side-chains 77 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 746 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 138 optimal weight: 2.9990 chunk 38 optimal weight: 0.0270 chunk 54 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 0.3980 chunk 130 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN A 677 HIS B 540 ASN B 677 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.069616 restraints weight = 40364.982| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.77 r_work: 0.2740 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12932 Z= 0.101 Angle : 0.489 5.899 17656 Z= 0.248 Chirality : 0.042 0.187 1888 Planarity : 0.004 0.055 2324 Dihedral : 4.544 58.642 1738 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.98 % Allowed : 8.80 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.22), residues: 1576 helix: 1.99 (0.20), residues: 690 sheet: 0.19 (0.40), residues: 170 loop : -0.15 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 758 TYR 0.010 0.001 TYR B 71 PHE 0.008 0.001 PHE A 125 TRP 0.012 0.001 TRP B 295 HIS 0.006 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (12932) covalent geometry : angle 0.48940 / 0.25 (17656) hydrogen bonds : bond 0.02828 / 2.00 ( 547) hydrogen bonds : angle 3.74410 / 2.74 ( 1516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.363 Fit side-chains REVERT: A 537 GLN cc_start: 0.8595 (tt0) cc_final: 0.8037 (pp30) REVERT: A 585 TYR cc_start: 0.8921 (m-80) cc_final: 0.8716 (m-80) REVERT: A 674 GLU cc_start: 0.8116 (mp0) cc_final: 0.7843 (mp0) REVERT: A 721 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7723 (mmp-170) REVERT: A 734 GLU cc_start: 0.8520 (tt0) cc_final: 0.8284 (tt0) REVERT: A 749 ASP cc_start: 0.7966 (m-30) cc_final: 0.7644 (m-30) REVERT: A 791 GLN cc_start: 0.8967 (mt0) cc_final: 0.8757 (mm110) REVERT: B 277 GLU cc_start: 0.8255 (pp20) cc_final: 0.8043 (pp20) REVERT: B 516 GLU cc_start: 0.8346 (mp0) cc_final: 0.7845 (mp0) REVERT: B 721 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8286 (mmp-170) REVERT: B 734 GLU cc_start: 0.8437 (tt0) cc_final: 0.8171 (tt0) REVERT: B 738 ARG cc_start: 0.8798 (mmp80) cc_final: 0.8452 (ttm-80) outliers start: 13 outliers final: 8 residues processed: 91 average time/residue: 0.5176 time to fit residues: 51.9704 Evaluate side-chains 77 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 721 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.0030 chunk 131 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 ASN A 677 HIS B 537 GLN B 677 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.069275 restraints weight = 51864.708| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 4.21 r_work: 0.2722 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12932 Z= 0.101 Angle : 0.483 5.196 17656 Z= 0.245 Chirality : 0.042 0.186 1888 Planarity : 0.004 0.059 2324 Dihedral : 4.510 59.103 1738 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.13 % Allowed : 8.87 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.22), residues: 1576 helix: 2.01 (0.20), residues: 690 sheet: 0.21 (0.40), residues: 170 loop : -0.11 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 758 TYR 0.009 0.001 TYR B 492 PHE 0.012 0.001 PHE A 495 TRP 0.012 0.001 TRP B 295 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (12932) covalent geometry : angle 0.48349 / 0.24 (17656) hydrogen bonds : bond 0.02805 / 1.98 ( 547) hydrogen bonds : angle 3.69677 / 2.71 ( 1516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.477 Fit side-chains REVERT: A 474 GLU cc_start: 0.9042 (tp30) cc_final: 0.8387 (tp30) REVERT: A 537 GLN cc_start: 0.8650 (tt0) cc_final: 0.8073 (pp30) REVERT: A 540 ASN cc_start: 0.7123 (m-40) cc_final: 0.5949 (t0) REVERT: A 585 TYR cc_start: 0.8871 (m-80) cc_final: 0.8662 (m-80) REVERT: A 674 GLU cc_start: 0.8114 (mp0) cc_final: 0.7821 (mp0) REVERT: A 721 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7724 (mmp-170) REVERT: A 734 GLU cc_start: 0.8516 (tt0) cc_final: 0.8304 (tt0) REVERT: A 749 ASP cc_start: 0.7995 (m-30) cc_final: 0.7669 (m-30) REVERT: A 791 GLN cc_start: 0.8991 (mt0) cc_final: 0.8764 (mm110) REVERT: B 277 GLU cc_start: 0.8247 (pp20) cc_final: 0.8026 (pp20) REVERT: B 516 GLU cc_start: 0.8302 (mp0) cc_final: 0.8027 (mp0) REVERT: B 721 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8222 (mtp180) REVERT: B 734 GLU cc_start: 0.8476 (tt0) cc_final: 0.8207 (tt0) REVERT: B 738 ARG cc_start: 0.8809 (mmp80) cc_final: 0.8460 (ttm-80) outliers start: 15 outliers final: 10 residues processed: 83 average time/residue: 0.4957 time to fit residues: 45.7563 Evaluate side-chains 80 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 746 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 143 optimal weight: 0.0980 chunk 12 optimal weight: 0.0370 chunk 44 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 677 HIS B 540 ASN B 677 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.070063 restraints weight = 48658.952| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.10 r_work: 0.2756 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12932 Z= 0.094 Angle : 0.476 5.432 17656 Z= 0.241 Chirality : 0.042 0.184 1888 Planarity : 0.004 0.062 2324 Dihedral : 4.446 56.639 1738 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.20 % Allowed : 8.80 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.22), residues: 1576 helix: 2.12 (0.20), residues: 678 sheet: 0.28 (0.40), residues: 170 loop : 0.02 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 758 TYR 0.009 0.001 TYR B 492 PHE 0.017 0.001 PHE A 495 TRP 0.012 0.001 TRP B 295 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.09 (12932) covalent geometry : angle 0.47561 / 0.24 (17656) hydrogen bonds : bond 0.02695 / 1.91 ( 547) hydrogen bonds : angle 3.64922 / 2.67 ( 1516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.297 Fit side-chains REVERT: A 474 GLU cc_start: 0.9021 (tp30) cc_final: 0.8391 (tp30) REVERT: A 537 GLN cc_start: 0.8597 (tt0) cc_final: 0.8064 (pp30) REVERT: A 540 ASN cc_start: 0.7017 (m-40) cc_final: 0.5809 (t0) REVERT: A 674 GLU cc_start: 0.8110 (mp0) cc_final: 0.7808 (mp0) REVERT: A 721 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7700 (mmp-170) REVERT: A 734 GLU cc_start: 0.8535 (tt0) cc_final: 0.8091 (tt0) REVERT: A 738 ARG cc_start: 0.8741 (ttm-80) cc_final: 0.8372 (ttm-80) REVERT: A 749 ASP cc_start: 0.7988 (m-30) cc_final: 0.7666 (m-30) REVERT: A 791 GLN cc_start: 0.9016 (mt0) cc_final: 0.8754 (mm-40) REVERT: B 277 GLU cc_start: 0.8226 (pp20) cc_final: 0.8012 (pp20) REVERT: B 516 GLU cc_start: 0.8302 (mp0) cc_final: 0.8024 (mp0) REVERT: B 540 ASN cc_start: 0.7599 (m-40) cc_final: 0.6460 (t0) REVERT: B 721 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8256 (mtp180) REVERT: B 734 GLU cc_start: 0.8478 (tt0) cc_final: 0.8203 (tt0) REVERT: B 738 ARG cc_start: 0.8816 (mmp80) cc_final: 0.8459 (ttm-80) REVERT: B 791 GLN cc_start: 0.8998 (mt0) cc_final: 0.8757 (mt0) outliers start: 16 outliers final: 9 residues processed: 92 average time/residue: 0.4991 time to fit residues: 50.8816 Evaluate side-chains 79 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 746 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.0040 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 12 optimal weight: 0.0040 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 677 HIS B 677 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.070503 restraints weight = 41731.784| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.90 r_work: 0.2764 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12932 Z= 0.094 Angle : 0.478 6.381 17656 Z= 0.242 Chirality : 0.042 0.181 1888 Planarity : 0.004 0.064 2324 Dihedral : 4.441 55.122 1738 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.90 % Allowed : 9.40 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1576 helix: 2.15 (0.20), residues: 678 sheet: 0.31 (0.40), residues: 170 loop : 0.00 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 758 TYR 0.009 0.001 TYR B 480 PHE 0.022 0.001 PHE A 495 TRP 0.012 0.001 TRP B 295 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.09 (12932) covalent geometry : angle 0.47817 / 0.24 (17656) hydrogen bonds : bond 0.02661 / 1.88 ( 547) hydrogen bonds : angle 3.62421 / 2.65 ( 1516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.456 Fit side-chains REVERT: A 474 GLU cc_start: 0.9022 (tp30) cc_final: 0.8409 (tp30) REVERT: A 537 GLN cc_start: 0.8564 (tt0) cc_final: 0.8028 (pp30) REVERT: A 540 ASN cc_start: 0.6902 (m-40) cc_final: 0.5760 (t0) REVERT: A 674 GLU cc_start: 0.8099 (mp0) cc_final: 0.7790 (mp0) REVERT: A 721 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7675 (mmp-170) REVERT: A 734 GLU cc_start: 0.8530 (tt0) cc_final: 0.8068 (tt0) REVERT: A 738 ARG cc_start: 0.8755 (ttm-80) cc_final: 0.8368 (ttm-80) REVERT: A 749 ASP cc_start: 0.7974 (m-30) cc_final: 0.7654 (m-30) REVERT: A 791 GLN cc_start: 0.9023 (mt0) cc_final: 0.8748 (mm-40) REVERT: B 277 GLU cc_start: 0.8214 (pp20) cc_final: 0.8012 (pp20) REVERT: B 516 GLU cc_start: 0.8291 (mp0) cc_final: 0.8011 (mp0) REVERT: B 540 ASN cc_start: 0.7613 (m-40) cc_final: 0.6434 (t0) REVERT: B 721 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8260 (mtp180) REVERT: B 734 GLU cc_start: 0.8458 (tt0) cc_final: 0.8179 (tt0) REVERT: B 738 ARG cc_start: 0.8792 (mmp80) cc_final: 0.8439 (ttm-80) REVERT: B 791 GLN cc_start: 0.8971 (mt0) cc_final: 0.8729 (mt0) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.5170 time to fit residues: 48.2148 Evaluate side-chains 81 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 746 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 86 optimal weight: 1.9990 chunk 111 optimal weight: 0.0970 chunk 12 optimal weight: 0.0770 chunk 23 optimal weight: 0.0670 chunk 90 optimal weight: 0.3980 chunk 3 optimal weight: 0.0010 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.0870 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 overall best weight: 0.0658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 730 ASN B 209 HIS B 677 HIS B 730 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.098751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.073135 restraints weight = 52869.994| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.35 r_work: 0.2839 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12932 Z= 0.085 Angle : 0.480 9.535 17656 Z= 0.240 Chirality : 0.041 0.171 1888 Planarity : 0.004 0.062 2324 Dihedral : 4.303 52.028 1738 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.60 % Allowed : 9.85 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.22), residues: 1576 helix: 2.15 (0.20), residues: 680 sheet: 0.37 (0.39), residues: 186 loop : 0.07 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 758 TYR 0.011 0.001 TYR B 480 PHE 0.013 0.001 PHE A 495 TRP 0.013 0.001 TRP B 295 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (12932) covalent geometry : angle 0.47978 / 0.24 (17656) hydrogen bonds : bond 0.02336 / 1.63 ( 547) hydrogen bonds : angle 3.55865 / 2.60 ( 1516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3705.52 seconds wall clock time: 64 minutes 2.66 seconds (3842.66 seconds total)