Starting phenix.real_space_refine on Fri Jul 3 02:11:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dau_46698/07_2026/9dau_46698.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dau_46698/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dau_46698/07_2026/9dau_46698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dau_46698/07_2026/9dau_46698.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dau_46698/07_2026/9dau_46698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dau_46698/07_2026/9dau_46698.map" } 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-dev-6108/lib/python3.11/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: 1.98, per 1000 atoms: 0.17 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: 0.68 Conformation dependent library (CDL) restraints added in 429.7 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: 0.22 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: 1.44 Time building geometry restraints manager: 0.99 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=" O4' TTP B 802 " ideal model delta sigma weight residual 1.405 1.599 -0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" C1' TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sigma weight residual 1.405 1.599 -0.194 2.00e-02 2.50e+03 9.42e+01 bond pdb=" C1' TTP B 802 " pdb=" C2' TTP B 802 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.40e+01 bond pdb=" C1' TTP A 801 " pdb=" C2' TTP A 801 " ideal model delta sigma weight residual 1.523 1.341 0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" C5 TTP A 801 " pdb=" C6 TTP A 801 " ideal model delta sigma weight residual 1.344 1.513 -0.169 2.00e-02 2.50e+03 7.18e+01 ... (remaining 11613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 15650 4.21 - 8.42: 83 8.42 - 12.63: 12 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 - 27.03: 6390 27.03 - 54.05: 582 54.05 - 81.08: 81 81.08 - 108.11: 9 108.11 - 135.13: 1 Dihedral angle restraints: 7063 sinusoidal: 2985 harmonic: 4078 Sorted by residual: dihedral pdb=" O1B DTP B 804 " pdb=" O3B DTP B 804 " pdb=" PB DTP B 804 " pdb=" PG DTP B 804 " ideal model delta sinusoidal sigma weight residual -60.07 75.06 -135.13 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" O1B DTP A 803 " pdb=" O3B DTP A 803 " pdb=" PB DTP A 803 " pdb=" PG DTP A 803 " ideal model delta sinusoidal sigma weight residual -60.07 45.32 -105.39 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" CA PRO A 397 " pdb=" C PRO A 397 " pdb=" N MET A 398 " pdb=" CA MET A 398 " ideal model delta harmonic sigma weight residual 180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 7060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1195 0.039 - 0.078: 378 0.078 - 0.117: 93 0.117 - 0.156: 18 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=" C3' TTP A 801 " pdb=" C2' TTP A 801 " pdb=" C4' TTP A 801 " pdb=" O3' TTP A 801 " both_signs ideal model delta sigma weight residual False -2.70 -2.55 -0.15 2.00e-01 2.50e+01 5.92e-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 ... (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: 0.920 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.300 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 0.194 11626 Z= 0.375 Angle : 0.874 21.048 15765 Z= 0.606 Chirality : 0.041 0.195 1685 Planarity : 0.004 0.064 2016 Dihedral : 19.391 135.134 4451 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/Z covalent geometry : bond 0.00687 / 0.37 (11618) covalent geometry : angle 0.87178 / 0.61 (15753) hydrogen bonds : bond 0.17842 / 11.96 ( 534) hydrogen bonds : angle 6.98882 / 5.12 ( 1539) metal coordination : bond 0.00349 / 0.16 ( 8) metal coordination : angle 2.53517 / 1.51 ( 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 : 0.360 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: 0.0736 time to fit residues: 37.9924 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 : 0.370 ------------------------------------------------------------------------------- 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... 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 623 HIS B 723 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083012 restraints weight = 21979.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.085895 restraints weight = 9567.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.087647 restraints weight = 5013.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088760 restraints weight = 3001.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.089498 restraints weight = 2030.624| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1276 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= 0.114 Angle : 0.525 5.837 15765 Z= 0.275 Chirality : 0.041 0.149 1685 Planarity : 0.004 0.062 2016 Dihedral : 11.030 101.652 1784 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.30 % Allowed : 31.71 % Favored : 63.00 % 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: 0.16 (0.23), residues: 1387 helix: 1.50 (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 0.006 0.000 ARG B 711 TYR 0.013 0.001 TYR A 557 PHE 0.022 0.001 PHE B 246 TRP 0.007 0.001 TRP A 546 HIS 0.005 0.001 HIS B 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (11618) covalent geometry : angle 0.51964 / 0.27 (15753) hydrogen bonds : bond 0.04281 / 2.84 ( 534) hydrogen bonds : angle 4.73268 / 3.53 ( 1539) metal coordination : bond 0.00391 / 0.19 ( 8) metal coordination : angle 2.78526 / 1.84 ( 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 407 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 343 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6295 (mmtt) cc_final: 0.5232 (mtmt) REVERT: A 74 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.7077 (pttm) REVERT: A 319 GLU cc_start: 0.7700 (mt-10) cc_final: 0.6959 (mt-10) REVERT: A 410 GLU cc_start: 0.8049 (pm20) cc_final: 0.7822 (pm20) REVERT: A 419 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.8091 (mtm-85) REVERT: A 420 MET cc_start: 0.8102 (pmm) cc_final: 0.7725 (pmm) REVERT: A 451 MET cc_start: 0.8590 (mmm) cc_final: 0.8382 (mmm) REVERT: A 505 LEU cc_start: 0.8548 (tt) cc_final: 0.7958 (pp) REVERT: A 521 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8635 (m-30) REVERT: A 558 SER cc_start: 0.9054 (m) cc_final: 0.8695 (t) REVERT: A 572 ASP cc_start: 0.8079 (t0) cc_final: 0.7838 (m-30) REVERT: A 586 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7857 (mt-10) REVERT: A 626 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7155 (mm-30) REVERT: A 629 VAL cc_start: 0.8909 (t) cc_final: 0.8694 (p) REVERT: A 666 GLU cc_start: 0.7929 (pt0) cc_final: 0.7610 (pt0) REVERT: A 707 MET cc_start: 0.8368 (pmm) cc_final: 0.8099 (pmm) REVERT: B 38 LYS cc_start: 0.7966 (tmtt) cc_final: 0.7460 (ttmt) REVERT: B 43 ILE cc_start: 0.7487 (mm) cc_final: 0.7116 (tp) REVERT: B 176 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8225 (t80) REVERT: B 204 LYS cc_start: 0.8883 (tttt) cc_final: 0.8603 (tttm) REVERT: B 253 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8561 (mp) REVERT: B 264 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7902 (tm-30) REVERT: B 291 GLU cc_start: 0.7808 (tp30) cc_final: 0.7334 (tp30) REVERT: B 319 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7255 (mt-10) REVERT: B 367 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8174 (mm110) REVERT: B 372 CYS cc_start: 0.8860 (t) cc_final: 0.8291 (t) REVERT: B 383 SER cc_start: 0.8751 (t) cc_final: 0.8399 (m) REVERT: B 458 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8155 (mp) REVERT: B 653 THR cc_start: 0.8802 (m) cc_final: 0.8526 (m) REVERT: B 729 TYR cc_start: 0.7599 (t80) cc_final: 0.7105 (t80) outliers start: 64 outliers final: 31 residues processed: 378 average time/residue: 0.0782 time to fit residues: 44.2972 Evaluate side-chains 361 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 325 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 74 LYS 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 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 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: 3.9990 chunk 41 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 66 optimal weight: 0.0770 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 HIS A 225 GLN A 254 ASN A 553 HIS A 623 HIS B 222 GLN B 593 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.089535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.077717 restraints weight = 22847.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.080373 restraints weight = 10206.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.082047 restraints weight = 5462.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083124 restraints weight = 3325.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.083834 restraints weight = 2271.974| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11626 Z= 0.226 Angle : 0.598 9.055 15765 Z= 0.314 Chirality : 0.044 0.185 1685 Planarity : 0.005 0.058 2016 Dihedral : 10.705 83.755 1743 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 7.28 % Allowed : 30.71 % 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: 0.04 (0.23), residues: 1387 helix: 1.43 (0.20), residues: 698 sheet: -1.90 (0.51), residues: 104 loop : -1.34 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 450 TYR 0.021 0.002 TYR A 557 PHE 0.024 0.002 PHE B 246 TRP 0.006 0.001 TRP B 546 HIS 0.005 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (11618) covalent geometry : angle 0.59141 / 0.31 (15753) hydrogen bonds : bond 0.05180 / 3.41 ( 534) hydrogen bonds : angle 4.70775 / 3.49 ( 1539) metal coordination : bond 0.00872 / 0.37 ( 8) metal coordination : angle 3.30066 / 2.07 ( 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 424 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 336 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6367 (mmtt) cc_final: 0.5207 (mtmt) REVERT: A 319 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6938 (mt-10) REVERT: A 410 GLU cc_start: 0.8115 (pm20) cc_final: 0.7903 (pm20) REVERT: A 420 MET cc_start: 0.8337 (pmm) cc_final: 0.8013 (pmm) REVERT: A 499 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8930 (mtt-85) REVERT: A 521 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8641 (m-30) REVERT: A 558 SER cc_start: 0.9034 (m) cc_final: 0.8681 (t) REVERT: A 572 ASP cc_start: 0.8057 (t0) cc_final: 0.7724 (m-30) REVERT: A 581 ASP cc_start: 0.7970 (t70) cc_final: 0.7581 (t0) REVERT: A 586 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 626 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7230 (mm-30) REVERT: A 629 VAL cc_start: 0.8994 (t) cc_final: 0.8779 (p) REVERT: A 666 GLU cc_start: 0.7955 (pt0) cc_final: 0.7559 (pt0) REVERT: A 711 ARG cc_start: 0.8124 (tpp-160) cc_final: 0.7870 (tpt170) REVERT: B 38 LYS cc_start: 0.8306 (tmtt) cc_final: 0.7843 (tttt) REVERT: B 176 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8369 (t80) REVERT: B 189 ASN cc_start: 0.8510 (t0) cc_final: 0.8302 (t0) REVERT: B 239 THR cc_start: 0.8924 (m) cc_final: 0.8580 (p) REVERT: B 253 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8660 (mp) REVERT: B 291 GLU cc_start: 0.7894 (tp30) cc_final: 0.7490 (tp30) REVERT: B 319 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7388 (mt-10) REVERT: B 367 GLN cc_start: 0.8471 (mm110) cc_final: 0.8271 (mm110) REVERT: B 383 SER cc_start: 0.8751 (t) cc_final: 0.8502 (m) REVERT: B 458 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8206 (mp) outliers start: 88 outliers final: 63 residues processed: 382 average time/residue: 0.0807 time to fit residues: 46.2565 Evaluate side-chains 387 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 319 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 505 LEU 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 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 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 486 LEU 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 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: 2.9990 chunk 7 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3168 r_free = 0.3168 target = 0.092048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.080098 restraints weight = 22208.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.082819 restraints weight = 9815.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.084515 restraints weight = 5212.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.085581 restraints weight = 3164.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.086246 restraints weight = 2163.430| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1857 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= 0.139 Angle : 0.536 6.794 15765 Z= 0.281 Chirality : 0.042 0.147 1685 Planarity : 0.004 0.060 2016 Dihedral : 10.222 81.284 1741 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 6.21 % Allowed : 31.54 % Favored : 62.25 % 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: 0.22 (0.23), residues: 1387 helix: 1.64 (0.20), residues: 696 sheet: -1.86 (0.51), residues: 103 loop : -1.33 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 450 TYR 0.015 0.001 TYR A 557 PHE 0.022 0.001 PHE B 246 TRP 0.004 0.001 TRP B 546 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11618) covalent geometry : angle 0.53076 / 0.28 (15753) hydrogen bonds : bond 0.04323 / 2.85 ( 534) hydrogen bonds : angle 4.47934 / 3.34 ( 1539) metal coordination : bond 0.00495 / 0.21 ( 8) metal coordination : angle 2.63830 / 1.71 ( 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: 75 poor density : 321 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6280 (mmtt) cc_final: 0.5136 (mtmt) REVERT: A 160 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7246 (mtt) REVERT: A 319 GLU cc_start: 0.7669 (mt-10) cc_final: 0.6848 (mt-10) REVERT: A 420 MET cc_start: 0.8308 (pmm) cc_final: 0.7903 (pmm) REVERT: A 521 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8608 (m-30) REVERT: A 558 SER cc_start: 0.9057 (m) cc_final: 0.8722 (t) REVERT: A 572 ASP cc_start: 0.7995 (t0) cc_final: 0.7693 (m-30) REVERT: A 586 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7820 (mt-10) REVERT: A 626 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7247 (mm-30) REVERT: A 629 VAL cc_start: 0.8955 (t) cc_final: 0.8738 (p) REVERT: A 666 GLU cc_start: 0.7946 (pt0) cc_final: 0.7504 (pt0) REVERT: A 696 CYS cc_start: 0.3389 (OUTLIER) cc_final: 0.2985 (m) REVERT: A 711 ARG cc_start: 0.8126 (tpp-160) cc_final: 0.7479 (tpt170) REVERT: B 38 LYS cc_start: 0.8176 (tmtt) cc_final: 0.7820 (tttt) REVERT: B 176 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8288 (t80) REVERT: B 189 ASN cc_start: 0.8510 (t0) cc_final: 0.8307 (t0) REVERT: B 253 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8611 (mp) REVERT: B 264 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7810 (tm-30) REVERT: B 291 GLU cc_start: 0.7881 (tp30) cc_final: 0.7472 (tp30) REVERT: B 319 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7309 (mt-10) REVERT: B 383 SER cc_start: 0.8719 (t) cc_final: 0.8428 (m) REVERT: B 458 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8206 (mp) outliers start: 75 outliers final: 49 residues processed: 363 average time/residue: 0.0798 time to fit residues: 43.7152 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 : 0.362 ------------------------------------------------------------------------------- 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 245 GLU Chi-restraints excluded: chain A residue 254 ASN 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 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 515 SER 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 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 696 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 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 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 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: 1.9990 chunk 35 optimal weight: 0.2980 chunk 134 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 254 ASN B 222 GLN B 367 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 = 0.3175 r_free = 0.3175 target = 0.092507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.080252 restraints weight = 22280.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083128 restraints weight = 9601.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.084889 restraints weight = 5015.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.086006 restraints weight = 3005.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.086751 restraints weight = 2035.586| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1971 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= 0.128 Angle : 0.530 7.510 15765 Z= 0.276 Chirality : 0.041 0.146 1685 Planarity : 0.004 0.059 2016 Dihedral : 9.904 78.005 1741 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.37 % Allowed : 30.96 % 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: 0.32 (0.23), residues: 1387 helix: 1.72 (0.20), residues: 699 sheet: -1.82 (0.51), residues: 103 loop : -1.30 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.016 0.001 TYR A 76 PHE 0.021 0.001 PHE B 246 TRP 0.005 0.001 TRP A 546 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11618) covalent geometry : angle 0.52557 / 0.28 (15753) hydrogen bonds : bond 0.04114 / 2.72 ( 534) hydrogen bonds : angle 4.38131 / 3.28 ( 1539) metal coordination : bond 0.00479 / 0.21 ( 8) metal coordination : angle 2.54238 / 1.67 ( 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 398 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 321 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6255 (mmtt) cc_final: 0.5113 (mtmt) REVERT: A 160 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7209 (mtt) REVERT: A 319 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6869 (mt-10) REVERT: A 420 MET cc_start: 0.8289 (pmm) cc_final: 0.7845 (pmm) REVERT: A 521 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8608 (m-30) REVERT: A 558 SER cc_start: 0.9050 (m) cc_final: 0.8756 (t) REVERT: A 572 ASP cc_start: 0.7971 (t0) cc_final: 0.7672 (m-30) REVERT: A 586 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7774 (mt-10) REVERT: A 626 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 629 VAL cc_start: 0.8947 (t) cc_final: 0.8716 (p) REVERT: A 666 GLU cc_start: 0.7902 (pt0) cc_final: 0.7472 (pt0) REVERT: A 707 MET cc_start: 0.8065 (pmm) cc_final: 0.7742 (pmm) REVERT: B 38 LYS cc_start: 0.8230 (tmtt) cc_final: 0.7911 (tttt) REVERT: B 176 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8283 (t80) REVERT: B 189 ASN cc_start: 0.8516 (t0) cc_final: 0.8278 (t0) REVERT: B 253 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8588 (mp) REVERT: B 264 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7694 (tm-30) REVERT: B 291 GLU cc_start: 0.7884 (tp30) cc_final: 0.7479 (tp30) REVERT: B 319 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7275 (mt-10) REVERT: B 383 SER cc_start: 0.8676 (t) cc_final: 0.8364 (m) REVERT: B 458 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8218 (mp) REVERT: B 508 ILE cc_start: 0.8835 (pt) cc_final: 0.8390 (mt) REVERT: B 690 ASP cc_start: 0.7556 (t0) cc_final: 0.7294 (t0) outliers start: 77 outliers final: 53 residues processed: 361 average time/residue: 0.0745 time to fit residues: 40.8806 Evaluate side-chains 372 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 314 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 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 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 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 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 216 ILE Chi-restraints excluded: chain B residue 253 LEU 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 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 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 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: 1.9990 chunk 136 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3173 r_free = 0.3173 target = 0.092322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.080370 restraints weight = 22232.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.083112 restraints weight = 9836.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.084811 restraints weight = 5210.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.085866 restraints weight = 3160.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.086594 restraints weight = 2173.525| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11626 Z= 0.158 Angle : 0.549 8.004 15765 Z= 0.286 Chirality : 0.042 0.166 1685 Planarity : 0.004 0.061 2016 Dihedral : 9.682 77.868 1740 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.21 % Allowed : 31.29 % Favored : 62.50 % 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: 0.32 (0.23), residues: 1387 helix: 1.71 (0.20), residues: 696 sheet: -1.80 (0.51), residues: 103 loop : -1.28 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.019 0.001 TYR A 76 PHE 0.022 0.001 PHE B 246 TRP 0.005 0.001 TRP A 546 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (11618) covalent geometry : angle 0.54484 / 0.29 (15753) hydrogen bonds : bond 0.04339 / 2.86 ( 534) hydrogen bonds : angle 4.41841 / 3.30 ( 1539) metal coordination : bond 0.00619 / 0.26 ( 8) metal coordination : angle 2.63246 / 1.72 ( 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 394 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 319 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6330 (mmtt) cc_final: 0.5179 (mtmt) REVERT: A 53 LYS cc_start: 0.8385 (tttp) cc_final: 0.8152 (tppt) REVERT: A 160 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7264 (mtt) REVERT: A 225 GLN cc_start: 0.8111 (mt0) cc_final: 0.7876 (mt0) REVERT: A 319 GLU cc_start: 0.7688 (mt-10) cc_final: 0.6896 (mt-10) REVERT: A 420 MET cc_start: 0.8316 (pmm) cc_final: 0.7952 (pmm) REVERT: A 521 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8620 (m-30) REVERT: A 558 SER cc_start: 0.9064 (m) cc_final: 0.8742 (t) REVERT: A 572 ASP cc_start: 0.8080 (t0) cc_final: 0.7771 (m-30) REVERT: A 581 ASP cc_start: 0.8029 (t0) cc_final: 0.7636 (t0) REVERT: A 586 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7816 (mt-10) REVERT: A 626 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7251 (mm-30) REVERT: A 629 VAL cc_start: 0.8985 (t) cc_final: 0.8757 (p) REVERT: A 666 GLU cc_start: 0.7921 (pt0) cc_final: 0.7477 (pt0) REVERT: A 707 MET cc_start: 0.8004 (pmm) cc_final: 0.7683 (pmm) REVERT: B 38 LYS cc_start: 0.8293 (tmtt) cc_final: 0.7968 (tttt) REVERT: B 176 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8288 (t80) REVERT: B 189 ASN cc_start: 0.8504 (t0) cc_final: 0.8225 (t0) REVERT: B 253 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8606 (mp) REVERT: B 291 GLU cc_start: 0.7893 (tp30) cc_final: 0.7497 (tp30) REVERT: B 319 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7316 (mt-10) REVERT: B 383 SER cc_start: 0.8677 (t) cc_final: 0.8421 (m) REVERT: B 458 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8227 (mp) REVERT: B 508 ILE cc_start: 0.8823 (pt) cc_final: 0.8380 (mt) REVERT: B 690 ASP cc_start: 0.7613 (t0) cc_final: 0.7340 (t0) outliers start: 75 outliers final: 60 residues processed: 360 average time/residue: 0.0813 time to fit residues: 44.0673 Evaluate side-chains 381 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 316 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 160 MET 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 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 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 571 LEU Chi-restraints excluded: chain A residue 574 GLU 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 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 193 ILE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 253 LEU 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 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 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: 7.9990 chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 721 HIS 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 = 0.3177 r_free = 0.3177 target = 0.092680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.080469 restraints weight = 22195.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.083333 restraints weight = 9569.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.085109 restraints weight = 4995.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.086236 restraints weight = 2990.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086949 restraints weight = 2014.996| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11626 Z= 0.141 Angle : 0.542 8.319 15765 Z= 0.282 Chirality : 0.042 0.154 1685 Planarity : 0.004 0.062 2016 Dihedral : 9.353 83.599 1740 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 6.46 % Allowed : 31.37 % 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: 0.34 (0.23), residues: 1387 helix: 1.74 (0.20), residues: 695 sheet: -1.84 (0.51), residues: 103 loop : -1.27 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 419 TYR 0.018 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 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (11618) covalent geometry : angle 0.53713 / 0.28 (15753) hydrogen bonds : bond 0.04191 / 2.76 ( 534) hydrogen bonds : angle 4.36738 / 3.26 ( 1539) metal coordination : bond 0.00547 / 0.23 ( 8) metal coordination : angle 2.58538 / 1.67 ( 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 397 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 319 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6408 (mmtt) cc_final: 0.5239 (mtmt) REVERT: A 53 LYS cc_start: 0.8382 (tttp) cc_final: 0.8136 (tppt) REVERT: A 160 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7233 (mtt) REVERT: A 319 GLU cc_start: 0.7673 (mt-10) cc_final: 0.6869 (mt-10) REVERT: A 420 MET cc_start: 0.8301 (pmm) cc_final: 0.7963 (pmm) REVERT: A 521 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8601 (m-30) REVERT: A 558 SER cc_start: 0.9045 (m) cc_final: 0.8749 (t) REVERT: A 572 ASP cc_start: 0.8063 (t0) cc_final: 0.7752 (m-30) REVERT: A 586 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7764 (mt-10) REVERT: A 626 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7274 (mm-30) REVERT: A 629 VAL cc_start: 0.8960 (t) cc_final: 0.8726 (p) REVERT: A 666 GLU cc_start: 0.7884 (pt0) cc_final: 0.7425 (pt0) REVERT: A 707 MET cc_start: 0.7926 (pmm) cc_final: 0.7598 (pmm) REVERT: B 38 LYS cc_start: 0.8287 (tmtt) cc_final: 0.7997 (tttt) REVERT: B 176 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8285 (t80) REVERT: B 189 ASN cc_start: 0.8521 (t0) cc_final: 0.8201 (t0) REVERT: B 209 GLU cc_start: 0.7827 (pp20) cc_final: 0.7625 (pp20) REVERT: B 253 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8604 (mp) REVERT: B 264 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7970 (tm-30) REVERT: B 291 GLU cc_start: 0.7869 (tp30) cc_final: 0.7495 (tp30) REVERT: B 319 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7279 (mt-10) REVERT: B 383 SER cc_start: 0.8659 (t) cc_final: 0.8394 (m) REVERT: B 458 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8235 (mp) REVERT: B 690 ASP cc_start: 0.7630 (t0) cc_final: 0.7346 (t0) outliers start: 78 outliers final: 63 residues processed: 362 average time/residue: 0.0785 time to fit residues: 43.5865 Evaluate side-chains 385 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 317 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 161 LEU 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 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 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 486 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 574 GLU 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 243 ILE Chi-restraints excluded: chain B residue 253 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 13 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 721 HIS 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 = 0.3180 r_free = 0.3180 target = 0.092896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.081000 restraints weight = 21960.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.083734 restraints weight = 9715.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.085412 restraints weight = 5146.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.086482 restraints weight = 3121.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.087201 restraints weight = 2138.129| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11626 Z= 0.124 Angle : 0.547 8.530 15765 Z= 0.281 Chirality : 0.041 0.171 1685 Planarity : 0.004 0.064 2016 Dihedral : 9.065 79.702 1740 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 6.04 % Allowed : 31.79 % 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: 0.42 (0.23), residues: 1387 helix: 1.80 (0.20), residues: 695 sheet: -1.83 (0.51), residues: 103 loop : -1.20 (0.26), residues: 589 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 0.004 0.001 TRP A 546 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (11618) covalent geometry : angle 0.54037 / 0.28 (15753) hydrogen bonds : bond 0.04014 / 2.63 ( 534) hydrogen bonds : angle 4.30769 / 3.22 ( 1539) metal coordination : bond 0.00784 / 0.37 ( 8) metal coordination : angle 3.06638 / 2.14 ( 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 395 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 322 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6427 (mmtt) cc_final: 0.5285 (mtmt) REVERT: A 53 LYS cc_start: 0.8369 (tttp) cc_final: 0.8133 (tppt) REVERT: A 74 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7438 (pttm) REVERT: A 160 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7212 (mtt) REVERT: A 319 GLU cc_start: 0.7672 (mt-10) cc_final: 0.6856 (mt-10) REVERT: A 329 VAL cc_start: 0.9045 (t) cc_final: 0.8825 (p) REVERT: A 420 MET cc_start: 0.8320 (pmm) cc_final: 0.7929 (pmm) REVERT: A 521 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8602 (m-30) REVERT: A 558 SER cc_start: 0.9059 (m) cc_final: 0.8738 (t) REVERT: A 572 ASP cc_start: 0.8056 (t0) cc_final: 0.7746 (m-30) REVERT: A 581 ASP cc_start: 0.7949 (t0) cc_final: 0.7635 (t0) REVERT: A 586 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7784 (mt-10) REVERT: A 626 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 629 VAL cc_start: 0.8910 (t) cc_final: 0.8680 (p) REVERT: A 666 GLU cc_start: 0.7864 (pt0) cc_final: 0.7397 (pt0) REVERT: A 707 MET cc_start: 0.7874 (pmm) cc_final: 0.7547 (pmm) REVERT: B 38 LYS cc_start: 0.8288 (tmtt) cc_final: 0.8007 (tttt) REVERT: B 176 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8254 (t80) REVERT: B 189 ASN cc_start: 0.8513 (t0) cc_final: 0.8224 (t0) REVERT: B 209 GLU cc_start: 0.7822 (pp20) cc_final: 0.7613 (pp20) REVERT: B 253 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8566 (mp) REVERT: B 264 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7970 (tm-30) REVERT: B 291 GLU cc_start: 0.7875 (tp30) cc_final: 0.7501 (tp30) REVERT: B 319 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7264 (mt-10) REVERT: B 383 SER cc_start: 0.8650 (t) cc_final: 0.8378 (m) REVERT: B 458 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8219 (mp) REVERT: B 508 ILE cc_start: 0.8833 (pt) cc_final: 0.8404 (mt) REVERT: B 690 ASP cc_start: 0.7634 (t0) cc_final: 0.7333 (t0) outliers start: 73 outliers final: 59 residues processed: 363 average time/residue: 0.0770 time to fit residues: 42.7791 Evaluate side-chains 382 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 317 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 74 LYS 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 220 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 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 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 630 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 658 ASP 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 100 ASN 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 287 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 370 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 271 GLN A 721 HIS 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 = 0.3195 r_free = 0.3195 target = 0.093749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.081847 restraints weight = 21874.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.084582 restraints weight = 9683.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.086260 restraints weight = 5120.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.087339 restraints weight = 3103.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.088004 restraints weight = 2123.239| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2223 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= 0.115 Angle : 0.547 8.747 15765 Z= 0.280 Chirality : 0.041 0.143 1685 Planarity : 0.004 0.064 2016 Dihedral : 8.825 71.642 1740 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.55 % Allowed : 32.70 % 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: 0.50 (0.24), residues: 1387 helix: 1.86 (0.20), residues: 695 sheet: -1.79 (0.51), residues: 103 loop : -1.15 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 711 TYR 0.018 0.001 TYR A 76 PHE 0.019 0.001 PHE B 246 TRP 0.005 0.001 TRP A 546 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (11618) covalent geometry : angle 0.54021 / 0.28 (15753) hydrogen bonds : bond 0.03843 / 2.53 ( 534) hydrogen bonds : angle 4.26080 / 3.19 ( 1539) metal coordination : bond 0.00616 / 0.30 ( 8) metal coordination : angle 3.21589 / 2.29 ( 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 389 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 322 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6438 (mmtt) cc_final: 0.5318 (mtmt) REVERT: A 53 LYS cc_start: 0.8360 (tttp) cc_final: 0.8125 (tppt) REVERT: A 160 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7185 (mtt) REVERT: A 329 VAL cc_start: 0.9025 (t) cc_final: 0.8811 (p) REVERT: A 347 ILE cc_start: 0.9138 (mt) cc_final: 0.8913 (mt) REVERT: A 367 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7787 (mt0) REVERT: A 420 MET cc_start: 0.8311 (pmm) cc_final: 0.7822 (pmm) REVERT: A 521 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8605 (m-30) REVERT: A 558 SER cc_start: 0.9048 (m) cc_final: 0.8737 (t) REVERT: A 572 ASP cc_start: 0.8044 (t0) cc_final: 0.7727 (m-30) REVERT: A 581 ASP cc_start: 0.7981 (t0) cc_final: 0.7661 (t0) REVERT: A 586 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 626 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7240 (mm-30) REVERT: A 629 VAL cc_start: 0.8896 (t) cc_final: 0.8647 (p) REVERT: A 666 GLU cc_start: 0.7848 (pt0) cc_final: 0.7429 (pt0) REVERT: A 707 MET cc_start: 0.7746 (pmm) cc_final: 0.7406 (pmm) REVERT: B 38 LYS cc_start: 0.8253 (tmtt) cc_final: 0.7985 (tttt) REVERT: B 176 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8195 (t80) REVERT: B 189 ASN cc_start: 0.8492 (t0) cc_final: 0.8221 (t0) REVERT: B 209 GLU cc_start: 0.7800 (pp20) cc_final: 0.7589 (pp20) REVERT: B 253 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8544 (mp) REVERT: B 264 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7930 (tm-30) REVERT: B 291 GLU cc_start: 0.7845 (tp30) cc_final: 0.7493 (tp30) REVERT: B 319 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7254 (mt-10) REVERT: B 383 SER cc_start: 0.8628 (t) cc_final: 0.8334 (m) REVERT: B 458 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8196 (mp) REVERT: B 508 ILE cc_start: 0.8829 (pt) cc_final: 0.8406 (mt) REVERT: B 690 ASP cc_start: 0.7653 (t0) cc_final: 0.7356 (t0) outliers start: 67 outliers final: 52 residues processed: 357 average time/residue: 0.0723 time to fit residues: 39.7080 Evaluate side-chains 372 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 315 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 254 ASN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 ILE 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 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 630 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 722 MET 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 253 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 65 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 721 HIS B 222 GLN B 367 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 = 0.3172 r_free = 0.3172 target = 0.092288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.080019 restraints weight = 22176.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.082885 restraints weight = 9573.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.084660 restraints weight = 4996.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.085783 restraints weight = 2995.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.086511 restraints weight = 2024.244| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11626 Z= 0.164 Angle : 0.582 11.492 15765 Z= 0.298 Chirality : 0.043 0.156 1685 Planarity : 0.004 0.066 2016 Dihedral : 8.944 72.136 1739 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.38 % Allowed : 32.45 % 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: 0.41 (0.23), residues: 1387 helix: 1.77 (0.20), residues: 695 sheet: -1.81 (0.52), residues: 103 loop : -1.18 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 711 TYR 0.018 0.001 TYR A 76 PHE 0.022 0.001 PHE B 246 TRP 0.005 0.001 TRP A 546 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (11618) covalent geometry : angle 0.57417 / 0.30 (15753) hydrogen bonds : bond 0.04261 / 2.80 ( 534) hydrogen bonds : angle 4.35885 / 3.25 ( 1539) metal coordination : bond 0.00812 / 0.35 ( 8) metal coordination : angle 3.52534 / 2.50 ( 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 387 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 322 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.6485 (mmtt) cc_final: 0.5356 (mtmt) REVERT: A 53 LYS cc_start: 0.8371 (tttp) cc_final: 0.8128 (tppt) REVERT: A 160 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7275 (mtt) REVERT: A 319 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6875 (mt-10) REVERT: A 347 ILE cc_start: 0.9148 (mt) cc_final: 0.8933 (mt) REVERT: A 420 MET cc_start: 0.8302 (pmm) cc_final: 0.7848 (pmm) REVERT: A 521 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8618 (m-30) REVERT: A 558 SER cc_start: 0.9052 (m) cc_final: 0.8752 (t) REVERT: A 572 ASP cc_start: 0.8066 (t0) cc_final: 0.7752 (m-30) REVERT: A 581 ASP cc_start: 0.7995 (t0) cc_final: 0.7701 (t0) REVERT: A 586 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7805 (mt-10) REVERT: A 626 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7234 (mm-30) REVERT: A 629 VAL cc_start: 0.8968 (t) cc_final: 0.8718 (p) REVERT: A 666 GLU cc_start: 0.7845 (pt0) cc_final: 0.7398 (pt0) REVERT: A 707 MET cc_start: 0.7849 (pmm) cc_final: 0.7502 (pmm) REVERT: B 38 LYS cc_start: 0.8337 (tmtt) cc_final: 0.8038 (tttt) REVERT: B 176 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8260 (t80) REVERT: B 189 ASN cc_start: 0.8543 (t0) cc_final: 0.8244 (t0) REVERT: B 209 GLU cc_start: 0.7831 (pp20) cc_final: 0.7619 (pp20) REVERT: B 253 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8613 (mp) REVERT: B 264 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7995 (tm-30) REVERT: B 291 GLU cc_start: 0.7856 (tp30) cc_final: 0.7501 (tp30) REVERT: B 319 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 383 SER cc_start: 0.8643 (t) cc_final: 0.8386 (m) REVERT: B 458 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 508 ILE cc_start: 0.8851 (pt) cc_final: 0.8417 (mt) REVERT: B 690 ASP cc_start: 0.7652 (t0) cc_final: 0.7374 (t0) outliers start: 65 outliers final: 51 residues processed: 360 average time/residue: 0.0686 time to fit residues: 37.9003 Evaluate side-chains 377 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 321 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 185 THR Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 294 ILE 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 571 LEU Chi-restraints excluded: chain A residue 601 THR 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 176 PHE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 356 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 136 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 721 HIS 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 = 0.3205 r_free = 0.3205 target = 0.094324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.082127 restraints weight = 22057.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.085016 restraints weight = 9482.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.086773 restraints weight = 4926.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.087874 restraints weight = 2941.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.088611 restraints weight = 1990.680| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11626 Z= 0.119 Angle : 0.561 9.333 15765 Z= 0.288 Chirality : 0.041 0.144 1685 Planarity : 0.004 0.065 2016 Dihedral : 8.738 69.556 1739 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.64 % Allowed : 33.61 % 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: 0.50 (0.24), residues: 1387 helix: 1.86 (0.20), residues: 692 sheet: -1.77 (0.52), residues: 103 loop : -1.14 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 711 TYR 0.013 0.001 TYR A 557 PHE 0.020 0.001 PHE A 246 TRP 0.004 0.001 TRP A 546 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (11618) covalent geometry : angle 0.55414 / 0.29 (15753) hydrogen bonds : bond 0.03892 / 2.56 ( 534) hydrogen bonds : angle 4.26516 / 3.19 ( 1539) metal coordination : bond 0.00524 / 0.25 ( 8) metal coordination : angle 3.15293 / 2.19 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1716.12 seconds wall clock time: 30 minutes 33.69 seconds (1833.69 seconds total)