Starting phenix.real_space_refine on Wed Feb 4 15:23:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dau_46698/02_2026/9dau_46698.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dau_46698/02_2026/9dau_46698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dau_46698/02_2026/9dau_46698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dau_46698/02_2026/9dau_46698.map" model { file = "/net/cci-nas-00/data/ceres_data/9dau_46698/02_2026/9dau_46698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dau_46698/02_2026/9dau_46698.cif" } resolution = 3.6 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= 0.167 sd= 0.721 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 18 5.49 5 Mg 4 5.21 5 S 53 5.16 5 C 7154 2.51 5 N 1917 2.21 5 O 2220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11368 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5594 Classifications: {'peptide': 699} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 669} Chain breaks: 1 Chain: "B" Number of atoms: 5586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5586 Classifications: {'peptide': 698} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 667} Chain breaks: 2 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {' MG': 2, ' ZN': 1, 'DTP': 2, 'TTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {' MG': 2, ' ZN': 1, 'DTP': 2, 'TTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5036 SG CYS A 660 67.647 15.591 53.600 1.00 85.22 S ATOM 5063 SG CYS A 663 67.329 11.893 53.146 1.00 88.16 S ATOM 5184 SG CYS A 678 65.987 14.271 50.423 1.00 86.32 S ATOM 5205 SG CYS A 681 64.147 13.937 53.616 1.00 87.91 S ATOM 10622 SG CYS B 660 95.042 71.868 71.866 1.00101.15 S ATOM 10649 SG CYS B 663 97.763 73.924 73.442 1.00100.28 S ATOM 10770 SG CYS B 678 94.251 74.668 74.386 1.00103.05 S ATOM 10791 SG CYS B 681 95.448 75.633 70.937 1.00101.81 S Time building chain proxies: 2.60, per 1000 atoms: 0.23 Number of scatterers: 11368 At special positions: 0 Unit cell: (127.296, 90.688, 114.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 53 16.00 P 18 15.00 Mg 4 11.99 O 2220 8.00 N 1917 7.00 C 7154 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: 0.97 Conformation dependent library (CDL) restraints added in 581.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 681 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 678 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 663 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 660 " pdb=" ZN B 806 " pdb="ZN ZN B 806 " - pdb=" SG CYS B 663 " pdb="ZN ZN B 806 " - pdb=" SG CYS B 678 " pdb="ZN ZN B 806 " - pdb=" SG CYS B 681 " pdb="ZN ZN B 806 " - pdb=" SG CYS B 660 " Number of angles added : 12 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 13 sheets defined 54.8% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 28 through 42 removed outlier: 3.769A pdb=" N ILE A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 69 removed outlier: 3.801A pdb=" N THR A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 89 removed outlier: 4.128A pdb=" N ILE A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER A 80 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 110 removed outlier: 4.116A pdb=" N ASN A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 105 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 161 removed outlier: 3.803A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 194 through 201 Processing helix chain 'A' and resid 215 through 233 Processing helix chain 'A' and resid 242 through 266 Proline residue: A 249 - end of helix removed outlier: 3.540A pdb=" N GLU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 297 removed outlier: 3.718A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 333 removed outlier: 3.674A pdb=" N GLY A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 428 through 437 removed outlier: 3.577A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 Processing helix chain 'A' and resid 467 through 468 No H-bonds generated for 'chain 'A' and resid 467 through 468' Processing helix chain 'A' and resid 469 through 472 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.751A pdb=" N GLN A 494 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 519 removed outlier: 3.761A pdb=" N PHE A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 524 removed outlier: 4.314A pdb=" N THR A 524 " --> pdb=" O ASP A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 521 through 524' Processing helix chain 'A' and resid 525 through 551 Processing helix chain 'A' and resid 563 through 577 removed outlier: 3.660A pdb=" N CYS A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 610 through 616 removed outlier: 3.917A pdb=" N GLU A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 616 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 648 removed outlier: 4.569A pdb=" N ASP A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.727A pdb=" N GLU A 714 " --> pdb=" O GLY A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 41 Processing helix chain 'B' and resid 47 through 69 removed outlier: 3.561A pdb=" N GLU B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 89 removed outlier: 3.721A pdb=" N GLU B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 113 removed outlier: 3.853A pdb=" N GLU B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 140 through 161 removed outlier: 3.789A pdb=" N LYS B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 194 through 202 removed outlier: 3.543A pdb=" N MET B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 232 removed outlier: 3.623A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 266 Proline residue: B 249 - end of helix Processing helix chain 'B' and resid 270 through 295 Processing helix chain 'B' and resid 316 through 333 removed outlier: 3.928A pdb=" N GLY B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 428 through 436 Processing helix chain 'B' and resid 439 through 466 Processing helix chain 'B' and resid 467 through 468 No H-bonds generated for 'chain 'B' and resid 467 through 468' Processing helix chain 'B' and resid 469 through 472 Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.616A pdb=" N GLN B 494 " --> pdb=" O SER B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 519 removed outlier: 3.896A pdb=" N PHE B 517 " --> pdb=" O VAL B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 551 removed outlier: 3.618A pdb=" N LYS B 529 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 577 removed outlier: 4.149A pdb=" N ARG B 570 " --> pdb=" O ASP B 566 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 610 Processing helix chain 'B' and resid 610 through 616 removed outlier: 3.892A pdb=" N GLU B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 648 removed outlier: 4.541A pdb=" N ASP B 646 " --> pdb=" O ASP B 642 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG B 647 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 717 Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 176 removed outlier: 4.491A pdb=" N ASN A 421 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER A 504 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLY A 423 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY A 506 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 425 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 507 " --> pdb=" O TYR A 557 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 240 removed outlier: 6.697A pdb=" N CYS A 238 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLY A 310 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA A 240 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N THR A 307 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ILE A 347 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 309 " --> pdb=" O ILE A 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 381 through 382 removed outlier: 6.156A pdb=" N HIS A 623 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN A 654 " --> pdb=" O HIS A 623 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N CYS A 625 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 689 through 690 removed outlier: 6.932A pdb=" N GLU A 666 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 693 through 695 removed outlier: 3.594A pdb=" N LYS A 693 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 698 " --> pdb=" O THR A 695 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 176 removed outlier: 7.357A pdb=" N CYS B 191 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS B 238 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLY B 310 " --> pdb=" O CYS B 238 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA B 240 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR B 307 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ILE B 347 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 309 " --> pdb=" O ILE B 347 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 176 removed outlier: 4.386A pdb=" N ASN B 421 " --> pdb=" O THR B 502 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N SER B 504 " --> pdb=" O ASN B 421 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY B 423 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLY B 506 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 425 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL B 503 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR B 557 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU B 505 " --> pdb=" O TYR B 557 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AB1, first strand: chain 'B' and resid 381 through 382 removed outlier: 6.613A pdb=" N HIS B 623 " --> pdb=" O GLY B 652 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASN B 654 " --> pdb=" O HIS B 623 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS B 625 " --> pdb=" O ASN B 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 689 through 690 removed outlier: 6.652A pdb=" N GLU B 666 " --> pdb=" O LYS B 728 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 670 through 672 removed outlier: 3.777A pdb=" N THR B 670 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 677 " --> pdb=" O THR B 670 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 693 through 694 536 hydrogen bonds defined for protein. 1539 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: 1.89 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1900 1.27 - 1.41: 2934 1.41 - 1.54: 6623 1.54 - 1.68: 83 1.68 - 1.81: 78 Bond restraints: 11618 Sorted by residual: bond pdb=" C1' TTP B 802 " pdb=" C2' TTP B 802 " ideal model delta sigma weight residual 1.524 1.340 0.184 2.00e-02 2.50e+03 8.49e+01 bond pdb=" C1' TTP A 801 " pdb=" C2' TTP A 801 " ideal model delta sigma weight residual 1.524 1.341 0.183 2.00e-02 2.50e+03 8.40e+01 bond pdb=" C2 TTP B 802 " pdb=" N3 TTP B 802 " ideal model delta sigma weight residual 1.337 1.519 -0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" C2 TTP A 801 " pdb=" N3 TTP A 801 " ideal model delta sigma weight residual 1.337 1.519 -0.182 2.00e-02 2.50e+03 8.25e+01 bond pdb=" C1' TTP B 802 " pdb=" O4' TTP B 802 " ideal model delta sigma weight residual 1.426 1.599 -0.173 2.00e-02 2.50e+03 7.50e+01 ... (remaining 11613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 15675 4.21 - 8.42: 66 8.42 - 12.63: 4 12.63 - 16.84: 1 16.84 - 21.05: 7 Bond angle restraints: 15753 Sorted by residual: angle pdb=" PB DTP B 803 " pdb=" O3B DTP B 803 " pdb=" PG DTP B 803 " ideal model delta sigma weight residual 139.87 118.82 21.05 1.00e+00 1.00e+00 4.43e+02 angle pdb=" PB DTP A 802 " pdb=" O3B DTP A 802 " pdb=" PG DTP A 802 " ideal model delta sigma weight residual 139.87 118.94 20.93 1.00e+00 1.00e+00 4.38e+02 angle pdb=" PB DTP A 803 " pdb=" O3B DTP A 803 " pdb=" PG DTP A 803 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB DTP B 804 " pdb=" O3B DTP B 804 " pdb=" PG DTP B 804 " ideal model delta sigma weight residual 139.87 121.51 18.36 1.00e+00 1.00e+00 3.37e+02 angle pdb=" PA DTP A 802 " pdb=" O3A DTP A 802 " pdb=" PB DTP A 802 " ideal model delta sigma weight residual 136.83 118.91 17.92 1.00e+00 1.00e+00 3.21e+02 ... (remaining 15748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 6650 34.81 - 69.62: 341 69.62 - 104.43: 17 104.43 - 139.25: 4 139.25 - 174.06: 3 Dihedral angle restraints: 7015 sinusoidal: 2937 harmonic: 4078 Sorted by residual: dihedral pdb=" C5' TTP B 802 " pdb=" O5' TTP B 802 " pdb=" PA TTP B 802 " pdb=" O3A TTP B 802 " ideal model delta sinusoidal sigma weight residual 179.97 5.92 174.06 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' TTP A 801 " pdb=" O5' TTP A 801 " pdb=" PA TTP A 801 " pdb=" O3A TTP A 801 " ideal model delta sinusoidal sigma weight residual 179.97 15.55 164.43 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O2G TTP B 802 " pdb=" O3B TTP B 802 " pdb=" PG TTP B 802 " pdb=" PB TTP B 802 " ideal model delta sinusoidal sigma weight residual -180.00 -31.65 -148.35 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 7012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1195 0.039 - 0.078: 379 0.078 - 0.117: 94 0.117 - 0.156: 16 0.156 - 0.195: 1 Chirality restraints: 1685 Sorted by residual: chirality pdb=" CA ILE B 283 " pdb=" N ILE B 283 " pdb=" C ILE B 283 " pdb=" CB ILE B 283 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA GLN B 288 " pdb=" N GLN B 288 " pdb=" C GLN B 288 " pdb=" CB GLN B 288 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 1682 not shown) Planarity restraints: 2016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 182 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO A 183 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 581 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.83e+00 pdb=" C ASP A 581 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP A 581 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A 582 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 182 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO B 183 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.030 5.00e-02 4.00e+02 ... (remaining 2013 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 26 2.18 - 2.86: 4343 2.86 - 3.54: 16199 3.54 - 4.22: 25945 4.22 - 4.90: 46383 Nonbonded interactions: 92896 Sorted by model distance: nonbonded pdb=" O2A DTP B 804 " pdb=" O2G DTP B 804 " model vdw 1.501 3.040 nonbonded pdb=" OE1 GLN B 288 " pdb="MG MG B 805 " model vdw 1.649 2.170 nonbonded pdb=" O1A DTP A 802 " pdb=" O1B DTP A 803 " model vdw 1.736 3.040 nonbonded pdb=" O1A DTP A 802 " pdb="MG MG A 804 " model vdw 2.027 2.170 nonbonded pdb="MG MG B 801 " pdb=" O2G DTP B 804 " model vdw 2.093 2.170 ... (remaining 92891 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 19 or resid 23 or resid 25 through 118 or resid \ 138 through 732 or resid 803 or resid 805 through 806)) selection = (chain 'B' and (resid 15 through 16 or resid 20 through 732 or resid 803 or resi \ d 805 through 806)) } 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: 1.420 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.910 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.184 11626 Z= 0.381 Angle : 0.811 21.048 15765 Z= 0.597 Chirality : 0.041 0.195 1685 Planarity : 0.004 0.064 2016 Dihedral : 19.757 174.056 4403 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.89 % Allowed : 35.35 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.19 (0.24), residues: 1387 helix: 1.15 (0.21), residues: 681 sheet: -1.83 (0.47), residues: 116 loop : -1.28 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.022 0.001 TYR A 76 PHE 0.017 0.001 PHE B 246 TRP 0.012 0.001 TRP A 546 HIS 0.007 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00699 (11618) covalent geometry : angle 0.80873 (15753) hydrogen bonds : bond 0.17842 ( 534) hydrogen bonds : angle 6.98882 ( 1539) metal coordination : bond 0.00349 ( 8) metal coordination : angle 2.53517 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 317 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6482 (mmtt) cc_final: 0.5493 (mtmt) REVERT: A 160 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7127 (mtt) REVERT: A 319 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6895 (mt-10) REVERT: A 329 VAL cc_start: 0.9043 (p) cc_final: 0.8830 (t) REVERT: A 420 MET cc_start: 0.7986 (pmm) cc_final: 0.7618 (pmm) REVERT: A 558 SER cc_start: 0.8944 (m) cc_final: 0.8696 (t) REVERT: A 626 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7047 (mm-30) REVERT: A 629 VAL cc_start: 0.8934 (t) cc_final: 0.8690 (p) REVERT: B 34 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6711 (mp0) REVERT: B 98 TYR cc_start: 0.7511 (t80) cc_final: 0.7232 (t80) REVERT: B 204 LYS cc_start: 0.8869 (tttt) cc_final: 0.8607 (tttm) REVERT: B 264 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7832 (tm-30) REVERT: B 291 GLU cc_start: 0.7778 (tp30) cc_final: 0.7531 (tp30) REVERT: B 319 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7159 (mt-10) REVERT: B 729 TYR cc_start: 0.7491 (t80) cc_final: 0.6916 (t80) outliers start: 47 outliers final: 35 residues processed: 341 average time/residue: 0.0847 time to fit residues: 43.8400 Evaluate side-chains 341 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 305 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 515 SER Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 726 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 144 GLN A 217 GLN A 225 GLN A 254 ASN A 271 GLN A 303 GLN A 328 GLN A 367 GLN A 590 ASN A 680 ASN B 79 GLN B 100 ASN B 144 GLN B 177 HIS B 222 GLN B 593 HIS B 723 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.094994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.082643 restraints weight = 21994.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.085520 restraints weight = 9620.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.087298 restraints weight = 5064.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088428 restraints weight = 3036.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.089145 restraints weight = 2048.099| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11626 Z= 0.118 Angle : 0.541 6.261 15765 Z= 0.279 Chirality : 0.041 0.150 1685 Planarity : 0.004 0.062 2016 Dihedral : 12.318 148.706 1736 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.13 % Allowed : 31.95 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: 0.17 (0.23), residues: 1387 helix: 1.51 (0.20), residues: 701 sheet: -1.89 (0.48), residues: 110 loop : -1.25 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 401 TYR 0.015 0.001 TYR B 292 PHE 0.021 0.001 PHE B 246 TRP 0.007 0.001 TRP B 546 HIS 0.005 0.001 HIS B 712 Details of bonding type rmsd covalent geometry : bond 0.00260 (11618) covalent geometry : angle 0.53602 (15753) hydrogen bonds : bond 0.04412 ( 534) hydrogen bonds : angle 4.77530 ( 1539) metal coordination : bond 0.00407 ( 8) metal coordination : angle 2.71416 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 338 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6281 (mmtt) cc_final: 0.5218 (mtmt) REVERT: A 102 ARG cc_start: 0.8836 (tpt170) cc_final: 0.8624 (tpt170) REVERT: A 319 GLU cc_start: 0.7705 (mt-10) cc_final: 0.6945 (mt-10) REVERT: A 410 GLU cc_start: 0.8060 (pm20) cc_final: 0.7831 (pm20) REVERT: A 419 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.8146 (mtm-85) REVERT: A 420 MET cc_start: 0.8106 (pmm) cc_final: 0.7707 (pmm) REVERT: A 450 ARG cc_start: 0.8450 (mmt90) cc_final: 0.8211 (mmt90) REVERT: A 505 LEU cc_start: 0.8541 (tt) cc_final: 0.7950 (pp) REVERT: A 521 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8632 (m-30) REVERT: A 558 SER cc_start: 0.9048 (m) cc_final: 0.8694 (t) REVERT: A 572 ASP cc_start: 0.8083 (t0) cc_final: 0.7854 (m-30) REVERT: A 586 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7869 (mt-10) REVERT: A 626 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7135 (mm-30) REVERT: A 629 VAL cc_start: 0.8908 (t) cc_final: 0.8694 (p) REVERT: A 666 GLU cc_start: 0.7931 (pt0) cc_final: 0.7622 (pt0) REVERT: A 707 MET cc_start: 0.8385 (pmm) cc_final: 0.8112 (pmm) REVERT: B 38 LYS cc_start: 0.7981 (tmtt) cc_final: 0.7464 (ttmt) REVERT: B 43 ILE cc_start: 0.7484 (mm) cc_final: 0.7112 (tp) REVERT: B 176 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8223 (t80) REVERT: B 177 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7701 (m-70) REVERT: B 204 LYS cc_start: 0.8872 (tttt) cc_final: 0.8593 (tttm) REVERT: B 253 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8571 (mp) REVERT: B 264 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7902 (tm-30) REVERT: B 291 GLU cc_start: 0.7797 (tp30) cc_final: 0.7342 (tp30) REVERT: B 319 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7284 (mt-10) REVERT: B 372 CYS cc_start: 0.8861 (t) cc_final: 0.8287 (t) REVERT: B 383 SER cc_start: 0.8761 (t) cc_final: 0.8402 (m) REVERT: B 395 LYS cc_start: 0.8688 (ptpp) cc_final: 0.8467 (ptpp) REVERT: B 458 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 562 GLU cc_start: 0.6805 (tt0) cc_final: 0.6168 (pm20) REVERT: B 729 TYR cc_start: 0.7586 (t80) cc_final: 0.7091 (t80) outliers start: 62 outliers final: 32 residues processed: 374 average time/residue: 0.0841 time to fit residues: 47.1258 Evaluate side-chains 358 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 321 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 484 GLN Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 378 TYR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 225 GLN A 254 ASN A 553 HIS A 623 HIS B 222 GLN B 367 GLN B 593 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.089236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.077361 restraints weight = 22591.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.080027 restraints weight = 9985.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.081691 restraints weight = 5314.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.082749 restraints weight = 3242.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.083461 restraints weight = 2229.824| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11626 Z= 0.251 Angle : 0.628 9.091 15765 Z= 0.326 Chirality : 0.045 0.182 1685 Planarity : 0.005 0.058 2016 Dihedral : 11.803 131.910 1695 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 7.20 % Allowed : 30.88 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: 0.01 (0.23), residues: 1387 helix: 1.41 (0.20), residues: 698 sheet: -1.91 (0.50), residues: 104 loop : -1.37 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 711 TYR 0.023 0.002 TYR A 557 PHE 0.025 0.002 PHE B 246 TRP 0.007 0.001 TRP B 546 HIS 0.021 0.002 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00569 (11618) covalent geometry : angle 0.62111 (15753) hydrogen bonds : bond 0.05272 ( 534) hydrogen bonds : angle 4.75873 ( 1539) metal coordination : bond 0.00989 ( 8) metal coordination : angle 3.46979 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 332 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6389 (mmtt) cc_final: 0.5223 (mtmt) REVERT: A 319 GLU cc_start: 0.7742 (mt-10) cc_final: 0.6967 (mt-10) REVERT: A 410 GLU cc_start: 0.8099 (pm20) cc_final: 0.7875 (pm20) REVERT: A 419 ARG cc_start: 0.8568 (mtm-85) cc_final: 0.8247 (mtm-85) REVERT: A 420 MET cc_start: 0.8336 (pmm) cc_final: 0.8062 (pmm) REVERT: A 499 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8939 (mtt-85) REVERT: A 521 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8649 (m-30) REVERT: A 558 SER cc_start: 0.9044 (m) cc_final: 0.8687 (t) REVERT: A 572 ASP cc_start: 0.8075 (t0) cc_final: 0.7773 (m-30) REVERT: A 581 ASP cc_start: 0.7974 (t70) cc_final: 0.7610 (t0) REVERT: A 626 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7271 (mm-30) REVERT: A 629 VAL cc_start: 0.9020 (t) cc_final: 0.8799 (p) REVERT: A 666 GLU cc_start: 0.7951 (pt0) cc_final: 0.7597 (pt0) REVERT: A 711 ARG cc_start: 0.8111 (tpp-160) cc_final: 0.7854 (tpt170) REVERT: B 38 LYS cc_start: 0.8305 (tmtt) cc_final: 0.7827 (tttt) REVERT: B 189 ASN cc_start: 0.8489 (t0) cc_final: 0.8282 (t0) REVERT: B 239 THR cc_start: 0.8957 (m) cc_final: 0.8599 (p) REVERT: B 253 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8707 (mp) REVERT: B 291 GLU cc_start: 0.7866 (tp30) cc_final: 0.7468 (tp30) REVERT: B 319 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7399 (mt-10) REVERT: B 383 SER cc_start: 0.8739 (t) cc_final: 0.8500 (m) REVERT: B 458 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8242 (mp) outliers start: 87 outliers final: 64 residues processed: 378 average time/residue: 0.0820 time to fit residues: 46.4848 Evaluate side-chains 393 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 325 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 489 CYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 716 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 45 optimal weight: 0.0670 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 254 ASN A 590 ASN B 222 GLN B 593 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.080012 restraints weight = 22243.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.082846 restraints weight = 9626.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.084608 restraints weight = 5049.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.085738 restraints weight = 3029.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.086456 restraints weight = 2045.937| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11626 Z= 0.143 Angle : 0.556 6.814 15765 Z= 0.286 Chirality : 0.042 0.150 1685 Planarity : 0.004 0.060 2016 Dihedral : 11.325 139.686 1693 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 6.29 % Allowed : 31.71 % Favored : 62.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: 0.25 (0.23), residues: 1387 helix: 1.66 (0.20), residues: 696 sheet: -1.88 (0.51), residues: 103 loop : -1.31 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 419 TYR 0.015 0.001 TYR A 557 PHE 0.023 0.001 PHE B 246 TRP 0.004 0.001 TRP B 546 HIS 0.004 0.001 HIS B 712 Details of bonding type rmsd covalent geometry : bond 0.00328 (11618) covalent geometry : angle 0.55075 (15753) hydrogen bonds : bond 0.04359 ( 534) hydrogen bonds : angle 4.46940 ( 1539) metal coordination : bond 0.00520 ( 8) metal coordination : angle 2.75273 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 320 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6297 (mmtt) cc_final: 0.5136 (mtmt) REVERT: A 160 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7226 (mtt) REVERT: A 319 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6881 (mt-10) REVERT: A 419 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8213 (mtm-85) REVERT: A 420 MET cc_start: 0.8305 (pmm) cc_final: 0.7948 (pmm) REVERT: A 450 ARG cc_start: 0.8430 (mmt90) cc_final: 0.8227 (mmt90) REVERT: A 505 LEU cc_start: 0.8642 (tt) cc_final: 0.8344 (tt) REVERT: A 521 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8604 (m-30) REVERT: A 558 SER cc_start: 0.9063 (m) cc_final: 0.8716 (t) REVERT: A 572 ASP cc_start: 0.8010 (t0) cc_final: 0.7724 (m-30) REVERT: A 586 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7829 (mt-10) REVERT: A 626 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7240 (mm-30) REVERT: A 629 VAL cc_start: 0.8960 (t) cc_final: 0.8738 (p) REVERT: A 666 GLU cc_start: 0.7940 (pt0) cc_final: 0.7511 (pt0) REVERT: A 711 ARG cc_start: 0.8114 (tpp-160) cc_final: 0.7861 (tpt170) REVERT: B 38 LYS cc_start: 0.8135 (tmtt) cc_final: 0.7773 (tttt) REVERT: B 189 ASN cc_start: 0.8503 (t0) cc_final: 0.8268 (t0) REVERT: B 253 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8635 (mp) REVERT: B 264 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 291 GLU cc_start: 0.7862 (tp30) cc_final: 0.7469 (tp30) REVERT: B 319 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7303 (mt-10) REVERT: B 383 SER cc_start: 0.8694 (t) cc_final: 0.8420 (m) REVERT: B 458 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8229 (mp) REVERT: B 659 LYS cc_start: 0.8286 (tttt) cc_final: 0.8030 (tttm) outliers start: 76 outliers final: 50 residues processed: 365 average time/residue: 0.0862 time to fit residues: 47.3650 Evaluate side-chains 369 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 716 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 254 ASN B 222 GLN B 593 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.093463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.081545 restraints weight = 22210.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.084264 restraints weight = 9806.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.085952 restraints weight = 5201.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.087043 restraints weight = 3153.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.087736 restraints weight = 2153.446| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11626 Z= 0.122 Angle : 0.541 7.249 15765 Z= 0.278 Chirality : 0.041 0.157 1685 Planarity : 0.004 0.059 2016 Dihedral : 10.897 147.695 1693 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 6.04 % Allowed : 31.62 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: 0.35 (0.24), residues: 1387 helix: 1.75 (0.20), residues: 699 sheet: -1.91 (0.51), residues: 104 loop : -1.26 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.015 0.001 TYR A 76 PHE 0.021 0.001 PHE B 246 TRP 0.004 0.001 TRP A 546 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd covalent geometry : bond 0.00279 (11618) covalent geometry : angle 0.53648 (15753) hydrogen bonds : bond 0.04074 ( 534) hydrogen bonds : angle 4.35872 ( 1539) metal coordination : bond 0.00440 ( 8) metal coordination : angle 2.56185 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 323 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6414 (mmtt) cc_final: 0.5237 (mtmt) REVERT: A 160 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7191 (mtt) REVERT: A 319 GLU cc_start: 0.7673 (mt-10) cc_final: 0.6874 (mt-10) REVERT: A 420 MET cc_start: 0.8322 (pmm) cc_final: 0.7984 (pmm) REVERT: A 451 MET cc_start: 0.8646 (mmm) cc_final: 0.8406 (mmm) REVERT: A 521 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8622 (m-30) REVERT: A 558 SER cc_start: 0.9065 (m) cc_final: 0.8757 (t) REVERT: A 572 ASP cc_start: 0.8072 (t0) cc_final: 0.7746 (m-30) REVERT: A 586 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7792 (mt-10) REVERT: A 626 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7249 (mm-30) REVERT: A 629 VAL cc_start: 0.8941 (t) cc_final: 0.8701 (p) REVERT: A 666 GLU cc_start: 0.7911 (pt0) cc_final: 0.7489 (pt0) REVERT: A 707 MET cc_start: 0.8007 (pmm) cc_final: 0.7695 (pmm) REVERT: A 711 ARG cc_start: 0.8076 (tpp-160) cc_final: 0.7794 (tpt170) REVERT: B 38 LYS cc_start: 0.8214 (tmtt) cc_final: 0.7877 (tttt) REVERT: B 176 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8241 (t80) REVERT: B 189 ASN cc_start: 0.8489 (t0) cc_final: 0.8242 (t0) REVERT: B 253 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8573 (mp) REVERT: B 264 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7692 (tm-30) REVERT: B 291 GLU cc_start: 0.7856 (tp30) cc_final: 0.7465 (tp30) REVERT: B 319 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7279 (mt-10) REVERT: B 383 SER cc_start: 0.8656 (t) cc_final: 0.8383 (m) REVERT: B 458 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8193 (mp) REVERT: B 508 ILE cc_start: 0.8820 (pt) cc_final: 0.8377 (mt) REVERT: B 659 LYS cc_start: 0.8268 (tttt) cc_final: 0.8004 (tttm) REVERT: B 690 ASP cc_start: 0.7557 (t0) cc_final: 0.7289 (t0) outliers start: 73 outliers final: 50 residues processed: 360 average time/residue: 0.0802 time to fit residues: 43.8741 Evaluate side-chains 371 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 716 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 64 optimal weight: 2.9990 chunk 136 optimal weight: 0.0020 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 254 ASN B 222 GLN B 593 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.082700 restraints weight = 22147.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.085577 restraints weight = 9526.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.087345 restraints weight = 4965.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088479 restraints weight = 2968.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.089226 restraints weight = 1997.837| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11626 Z= 0.111 Angle : 0.531 7.530 15765 Z= 0.272 Chirality : 0.041 0.154 1685 Planarity : 0.004 0.059 2016 Dihedral : 10.399 149.777 1693 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.71 % Allowed : 31.62 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: 0.49 (0.24), residues: 1387 helix: 1.84 (0.20), residues: 695 sheet: -1.80 (0.51), residues: 104 loop : -1.15 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 450 TYR 0.017 0.001 TYR A 76 PHE 0.020 0.001 PHE A 246 TRP 0.003 0.001 TRP B 546 HIS 0.003 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00251 (11618) covalent geometry : angle 0.52725 (15753) hydrogen bonds : bond 0.03838 ( 534) hydrogen bonds : angle 4.28867 ( 1539) metal coordination : bond 0.00365 ( 8) metal coordination : angle 2.45907 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 319 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6373 (mmtt) cc_final: 0.5225 (mtmt) REVERT: A 53 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8142 (tppt) REVERT: A 160 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7151 (mtt) REVERT: A 329 VAL cc_start: 0.9038 (t) cc_final: 0.8807 (p) REVERT: A 420 MET cc_start: 0.8269 (pmm) cc_final: 0.7838 (pmm) REVERT: A 521 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8607 (m-30) REVERT: A 558 SER cc_start: 0.9056 (m) cc_final: 0.8757 (t) REVERT: A 572 ASP cc_start: 0.8041 (t0) cc_final: 0.7733 (m-30) REVERT: A 586 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7793 (mt-10) REVERT: A 626 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7269 (mm-30) REVERT: A 629 VAL cc_start: 0.8904 (t) cc_final: 0.8667 (p) REVERT: A 666 GLU cc_start: 0.7895 (pt0) cc_final: 0.7468 (pt0) REVERT: A 707 MET cc_start: 0.7806 (pmm) cc_final: 0.7512 (pmm) REVERT: B 38 LYS cc_start: 0.8180 (tmtt) cc_final: 0.7888 (tttt) REVERT: B 176 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8190 (t80) REVERT: B 189 ASN cc_start: 0.8486 (t0) cc_final: 0.8236 (t0) REVERT: B 253 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8539 (mp) REVERT: B 264 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7704 (tm-30) REVERT: B 291 GLU cc_start: 0.7810 (tp30) cc_final: 0.7449 (tp30) REVERT: B 319 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7234 (mt-10) REVERT: B 383 SER cc_start: 0.8651 (t) cc_final: 0.8349 (m) REVERT: B 458 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8210 (mp) REVERT: B 508 ILE cc_start: 0.8809 (pt) cc_final: 0.8397 (mt) REVERT: B 659 LYS cc_start: 0.8284 (tttt) cc_final: 0.8033 (tttm) REVERT: B 690 ASP cc_start: 0.7562 (t0) cc_final: 0.7289 (t0) outliers start: 69 outliers final: 52 residues processed: 358 average time/residue: 0.0834 time to fit residues: 45.5599 Evaluate side-chains 374 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 316 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 484 GLN Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 716 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 222 GLN B 593 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.093271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.081048 restraints weight = 22191.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.083930 restraints weight = 9567.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.085681 restraints weight = 4993.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086801 restraints weight = 2991.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.087556 restraints weight = 2026.448| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11626 Z= 0.148 Angle : 0.548 6.672 15765 Z= 0.282 Chirality : 0.042 0.154 1685 Planarity : 0.004 0.062 2016 Dihedral : 10.265 149.493 1691 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.46 % Allowed : 30.88 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: 0.46 (0.24), residues: 1387 helix: 1.82 (0.20), residues: 696 sheet: -1.82 (0.51), residues: 104 loop : -1.17 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.016 0.001 TYR A 557 PHE 0.021 0.001 PHE B 246 TRP 0.004 0.001 TRP A 546 HIS 0.004 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00340 (11618) covalent geometry : angle 0.54324 (15753) hydrogen bonds : bond 0.04136 ( 534) hydrogen bonds : angle 4.32996 ( 1539) metal coordination : bond 0.00579 ( 8) metal coordination : angle 2.61894 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 318 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6414 (mmtt) cc_final: 0.5255 (mtmt) REVERT: A 53 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8156 (tppt) REVERT: A 160 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7271 (mtt) REVERT: A 319 GLU cc_start: 0.7698 (mt-10) cc_final: 0.6898 (mt-10) REVERT: A 420 MET cc_start: 0.8314 (pmm) cc_final: 0.8033 (pmm) REVERT: A 451 MET cc_start: 0.8642 (mmm) cc_final: 0.8380 (mmm) REVERT: A 521 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8624 (m-30) REVERT: A 558 SER cc_start: 0.9067 (m) cc_final: 0.8770 (t) REVERT: A 572 ASP cc_start: 0.8068 (t0) cc_final: 0.7740 (m-30) REVERT: A 581 ASP cc_start: 0.8007 (t0) cc_final: 0.7669 (t0) REVERT: A 586 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7807 (mt-10) REVERT: A 626 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7272 (mm-30) REVERT: A 629 VAL cc_start: 0.8926 (t) cc_final: 0.8699 (p) REVERT: A 666 GLU cc_start: 0.7864 (pt0) cc_final: 0.7411 (pt0) REVERT: A 707 MET cc_start: 0.7852 (pmm) cc_final: 0.7533 (pmm) REVERT: B 38 LYS cc_start: 0.8276 (tmtt) cc_final: 0.7965 (tttt) REVERT: B 176 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8252 (t80) REVERT: B 189 ASN cc_start: 0.8517 (t0) cc_final: 0.8239 (t0) REVERT: B 253 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8607 (mp) REVERT: B 264 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 291 GLU cc_start: 0.7840 (tp30) cc_final: 0.7488 (tp30) REVERT: B 319 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7282 (mt-10) REVERT: B 383 SER cc_start: 0.8653 (t) cc_final: 0.8383 (m) REVERT: B 458 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8243 (mp) REVERT: B 508 ILE cc_start: 0.8817 (pt) cc_final: 0.8401 (mt) REVERT: B 690 ASP cc_start: 0.7592 (t0) cc_final: 0.7320 (t0) outliers start: 78 outliers final: 59 residues processed: 358 average time/residue: 0.0852 time to fit residues: 46.8096 Evaluate side-chains 380 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 315 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 660 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 489 CYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 716 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 13 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 222 GLN B 301 ASN B 593 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.081277 restraints weight = 21929.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.084012 restraints weight = 9706.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.085705 restraints weight = 5140.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.086799 restraints weight = 3115.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.087455 restraints weight = 2124.694| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11626 Z= 0.126 Angle : 0.554 8.034 15765 Z= 0.281 Chirality : 0.041 0.145 1685 Planarity : 0.004 0.064 2016 Dihedral : 10.056 149.737 1691 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.13 % Allowed : 31.71 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: 0.48 (0.24), residues: 1387 helix: 1.83 (0.20), residues: 696 sheet: -1.79 (0.51), residues: 103 loop : -1.16 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 711 TYR 0.020 0.001 TYR B 292 PHE 0.020 0.001 PHE B 246 TRP 0.003 0.001 TRP B 546 HIS 0.005 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00291 (11618) covalent geometry : angle 0.54654 (15753) hydrogen bonds : bond 0.03976 ( 534) hydrogen bonds : angle 4.28093 ( 1539) metal coordination : bond 0.00833 ( 8) metal coordination : angle 3.22713 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 323 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6422 (mmtt) cc_final: 0.5274 (mtmt) REVERT: A 53 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8173 (tppt) REVERT: A 160 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7227 (mtt) REVERT: A 319 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6871 (mt-10) REVERT: A 347 ILE cc_start: 0.9203 (mt) cc_final: 0.8983 (mt) REVERT: A 367 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7799 (mt0) REVERT: A 420 MET cc_start: 0.8369 (pmm) cc_final: 0.8108 (pmm) REVERT: A 451 MET cc_start: 0.8611 (mmm) cc_final: 0.8346 (mmm) REVERT: A 521 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8615 (m-30) REVERT: A 558 SER cc_start: 0.9056 (m) cc_final: 0.8764 (t) REVERT: A 572 ASP cc_start: 0.8092 (t0) cc_final: 0.7777 (m-30) REVERT: A 581 ASP cc_start: 0.8006 (t0) cc_final: 0.7621 (t0) REVERT: A 586 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7801 (mt-10) REVERT: A 626 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7267 (mm-30) REVERT: A 629 VAL cc_start: 0.8922 (t) cc_final: 0.8671 (p) REVERT: A 666 GLU cc_start: 0.7883 (pt0) cc_final: 0.7431 (pt0) REVERT: A 707 MET cc_start: 0.7746 (pmm) cc_final: 0.7405 (pmm) REVERT: B 38 LYS cc_start: 0.8252 (tmtt) cc_final: 0.7975 (tttt) REVERT: B 176 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8214 (t80) REVERT: B 189 ASN cc_start: 0.8491 (t0) cc_final: 0.8224 (t0) REVERT: B 253 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8570 (mp) REVERT: B 264 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7681 (tm-30) REVERT: B 291 GLU cc_start: 0.7823 (tp30) cc_final: 0.7465 (tp30) REVERT: B 319 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7254 (mt-10) REVERT: B 383 SER cc_start: 0.8629 (t) cc_final: 0.8352 (m) REVERT: B 458 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8213 (mp) REVERT: B 508 ILE cc_start: 0.8814 (pt) cc_final: 0.8383 (mt) REVERT: B 690 ASP cc_start: 0.7630 (t0) cc_final: 0.7330 (t0) outliers start: 74 outliers final: 61 residues processed: 364 average time/residue: 0.0842 time to fit residues: 46.6652 Evaluate side-chains 384 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 317 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 489 CYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 716 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 37 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 254 ASN B 222 GLN B 593 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.094677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.082791 restraints weight = 21773.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.085532 restraints weight = 9620.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.087224 restraints weight = 5093.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088308 restraints weight = 3085.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.089018 restraints weight = 2105.871| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11626 Z= 0.120 Angle : 0.556 8.710 15765 Z= 0.283 Chirality : 0.041 0.143 1685 Planarity : 0.004 0.064 2016 Dihedral : 9.749 146.585 1691 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 6.04 % Allowed : 31.87 % Favored : 62.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: 0.52 (0.24), residues: 1387 helix: 1.86 (0.20), residues: 695 sheet: -1.82 (0.51), residues: 104 loop : -1.12 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 711 TYR 0.019 0.001 TYR A 76 PHE 0.020 0.001 PHE B 246 TRP 0.003 0.001 TRP B 546 HIS 0.006 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00278 (11618) covalent geometry : angle 0.54919 (15753) hydrogen bonds : bond 0.03923 ( 534) hydrogen bonds : angle 4.26364 ( 1539) metal coordination : bond 0.00624 ( 8) metal coordination : angle 3.21296 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 320 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6434 (mmtt) cc_final: 0.5309 (mtmt) REVERT: A 53 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8173 (tppt) REVERT: A 160 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7201 (mtt) REVERT: A 367 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7787 (mt0) REVERT: A 420 MET cc_start: 0.8412 (pmm) cc_final: 0.8155 (pmm) REVERT: A 451 MET cc_start: 0.8572 (mmm) cc_final: 0.8304 (mmm) REVERT: A 521 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8622 (m-30) REVERT: A 558 SER cc_start: 0.9063 (m) cc_final: 0.8792 (t) REVERT: A 572 ASP cc_start: 0.8090 (t0) cc_final: 0.7770 (m-30) REVERT: A 581 ASP cc_start: 0.8016 (t0) cc_final: 0.7672 (t0) REVERT: A 586 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7820 (mt-10) REVERT: A 626 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7239 (mm-30) REVERT: A 629 VAL cc_start: 0.8893 (t) cc_final: 0.8641 (p) REVERT: A 666 GLU cc_start: 0.7878 (pt0) cc_final: 0.7449 (pt0) REVERT: A 707 MET cc_start: 0.7676 (pmm) cc_final: 0.7321 (pmm) REVERT: B 38 LYS cc_start: 0.8266 (tmtt) cc_final: 0.8005 (tttt) REVERT: B 176 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8186 (t80) REVERT: B 189 ASN cc_start: 0.8470 (t0) cc_final: 0.8215 (t0) REVERT: B 253 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8541 (mp) REVERT: B 264 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 291 GLU cc_start: 0.7825 (tp30) cc_final: 0.7464 (tp30) REVERT: B 319 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7248 (mt-10) REVERT: B 383 SER cc_start: 0.8630 (t) cc_final: 0.8339 (m) REVERT: B 458 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8206 (mp) REVERT: B 508 ILE cc_start: 0.8816 (pt) cc_final: 0.8389 (mt) REVERT: B 690 ASP cc_start: 0.7644 (t0) cc_final: 0.7337 (t0) outliers start: 73 outliers final: 63 residues processed: 360 average time/residue: 0.0769 time to fit residues: 42.4393 Evaluate side-chains 389 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 320 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 484 GLN Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 489 CYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 716 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 65 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 254 ASN B 222 GLN B 593 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.082336 restraints weight = 22117.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.085198 restraints weight = 9506.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.086974 restraints weight = 4946.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.088117 restraints weight = 2952.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088845 restraints weight = 1987.995| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11626 Z= 0.128 Angle : 0.570 10.728 15765 Z= 0.289 Chirality : 0.042 0.146 1685 Planarity : 0.004 0.065 2016 Dihedral : 9.656 145.116 1691 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.71 % Allowed : 32.12 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: 0.52 (0.24), residues: 1387 helix: 1.88 (0.20), residues: 692 sheet: -1.80 (0.52), residues: 104 loop : -1.14 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 711 TYR 0.017 0.001 TYR B 292 PHE 0.020 0.001 PHE B 246 TRP 0.003 0.001 TRP B 546 HIS 0.006 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00297 (11618) covalent geometry : angle 0.56377 (15753) hydrogen bonds : bond 0.03967 ( 534) hydrogen bonds : angle 4.27793 ( 1539) metal coordination : bond 0.00606 ( 8) metal coordination : angle 3.20311 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 325 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6432 (mmtt) cc_final: 0.5319 (mtmt) REVERT: A 53 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8169 (tppt) REVERT: A 96 GLN cc_start: 0.7493 (tt0) cc_final: 0.7119 (tm-30) REVERT: A 160 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7202 (mtt) REVERT: A 319 GLU cc_start: 0.7670 (mt-10) cc_final: 0.6845 (mt-10) REVERT: A 367 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7813 (mt0) REVERT: A 420 MET cc_start: 0.8436 (pmm) cc_final: 0.8189 (pmm) REVERT: A 451 MET cc_start: 0.8588 (mmm) cc_final: 0.8334 (mmm) REVERT: A 521 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8613 (m-30) REVERT: A 557 TYR cc_start: 0.8735 (t80) cc_final: 0.8325 (t80) REVERT: A 558 SER cc_start: 0.9079 (m) cc_final: 0.8774 (t) REVERT: A 572 ASP cc_start: 0.8064 (t0) cc_final: 0.7750 (m-30) REVERT: A 581 ASP cc_start: 0.8033 (t0) cc_final: 0.7676 (t0) REVERT: A 586 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7788 (mt-10) REVERT: A 626 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7232 (mm-30) REVERT: A 629 VAL cc_start: 0.8901 (t) cc_final: 0.8647 (p) REVERT: A 666 GLU cc_start: 0.7840 (pt0) cc_final: 0.7382 (pt0) REVERT: A 707 MET cc_start: 0.7658 (pmm) cc_final: 0.7302 (pmm) REVERT: B 38 LYS cc_start: 0.8260 (tmtt) cc_final: 0.8004 (tttt) REVERT: B 176 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8212 (t80) REVERT: B 189 ASN cc_start: 0.8499 (t0) cc_final: 0.8239 (t0) REVERT: B 253 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 264 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7734 (tm-30) REVERT: B 291 GLU cc_start: 0.7792 (tp30) cc_final: 0.7443 (tp30) REVERT: B 319 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7247 (mt-10) REVERT: B 383 SER cc_start: 0.8636 (t) cc_final: 0.8279 (m) REVERT: B 458 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8232 (mp) REVERT: B 508 ILE cc_start: 0.8819 (pt) cc_final: 0.8393 (mt) REVERT: B 690 ASP cc_start: 0.7639 (t0) cc_final: 0.7339 (t0) outliers start: 69 outliers final: 62 residues processed: 364 average time/residue: 0.0758 time to fit residues: 41.7521 Evaluate side-chains 389 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 321 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 484 GLN Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 625 CYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 489 CYS Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 716 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 136 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 38 optimal weight: 0.0670 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN B 222 GLN B 593 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.093881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.081880 restraints weight = 22082.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.084626 restraints weight = 9710.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.086341 restraints weight = 5131.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.087435 restraints weight = 3096.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.088144 restraints weight = 2112.213| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11626 Z= 0.131 Angle : 0.585 16.561 15765 Z= 0.293 Chirality : 0.042 0.144 1685 Planarity : 0.004 0.065 2016 Dihedral : 9.633 143.697 1691 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.96 % Allowed : 32.28 % Favored : 61.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: 0.52 (0.24), residues: 1387 helix: 1.87 (0.20), residues: 692 sheet: -1.76 (0.52), residues: 104 loop : -1.13 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 711 TYR 0.015 0.001 TYR B 292 PHE 0.020 0.001 PHE B 246 TRP 0.003 0.001 TRP B 546 HIS 0.006 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00305 (11618) covalent geometry : angle 0.57867 (15753) hydrogen bonds : bond 0.03981 ( 534) hydrogen bonds : angle 4.28012 ( 1539) metal coordination : bond 0.00603 ( 8) metal coordination : angle 3.19948 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1825.53 seconds wall clock time: 32 minutes 27.22 seconds (1947.22 seconds total)