Starting phenix.real_space_refine on Sun Sep 13 14:09:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6on2_20133/09_2026/6on2_20133.cif Found real_map, /net/cci-nas-00/data/ceres_data/6on2_20133/09_2026/6on2_20133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6on2_20133/09_2026/6on2_20133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6on2_20133/09_2026/6on2_20133.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6on2_20133/09_2026/6on2_20133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6on2_20133/09_2026/6on2_20133.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6on2_20133/09_2026/6on2_20133.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6on2_20133/09_2026/6on2_20133.cif" } resolution = 3.0 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= 0.005 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 138 5.16 5 C 15268 2.51 5 N 4307 2.21 5 O 4616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24350 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4041 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 24, 'TRANS': 498} Chain: "B" Number of atoms: 4052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4052 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 24, 'TRANS': 499} Chain: "C" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4041 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 24, 'TRANS': 498} Chain: "D" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4001 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 24, 'TRANS': 493} Chain breaks: 1 Chain: "E" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4041 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 24, 'TRANS': 498} Chain: "F" Number of atoms: 3955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3955 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 24, 'TRANS': 487} Chain breaks: 1 Chain: "G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 36 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.75, per 1000 atoms: 0.24 Number of scatterers: 24350 At special positions: 0 Unit cell: (131.1, 136.85, 129.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 P 16 15.00 Mg 5 11.99 O 4616 8.00 N 4307 7.00 C 15268 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: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5786 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 28 sheets defined 47.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.590A pdb=" N ILE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 285 through 300 removed outlier: 3.743A pdb=" N THR A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 365 through 373 Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.772A pdb=" N LYS A 427 " --> pdb=" O GLN A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 444 removed outlier: 3.619A pdb=" N ALA A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.770A pdb=" N ASP A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.719A pdb=" N LYS A 509 " --> pdb=" O HIS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.652A pdb=" N ILE A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 561 Processing helix chain 'A' and resid 631 through 647 Processing helix chain 'A' and resid 657 through 660 Processing helix chain 'A' and resid 681 through 694 removed outlier: 3.552A pdb=" N THR A 686 " --> pdb=" O ILE A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.711A pdb=" N LYS A 722 " --> pdb=" O GLY A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 747 removed outlier: 5.057A pdb=" N ARG A 742 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 747 " --> pdb=" O LEU A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 755 Processing helix chain 'A' and resid 762 through 771 removed outlier: 3.732A pdb=" N VAL A 766 " --> pdb=" O ARG A 762 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 264 through 279 Processing helix chain 'B' and resid 285 through 299 Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 327 through 344 Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.960A pdb=" N SER B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 403 through 414 removed outlier: 4.303A pdb=" N ILE B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 428 Processing helix chain 'B' and resid 438 through 442 removed outlier: 3.823A pdb=" N GLU B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 451 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 505 through 515 removed outlier: 3.636A pdb=" N LYS B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 524 through 535 Processing helix chain 'B' and resid 541 through 563 Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 631 through 648 Processing helix chain 'B' and resid 657 through 661 Processing helix chain 'B' and resid 680 through 690 removed outlier: 3.545A pdb=" N MET B 684 " --> pdb=" O ALA B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 removed outlier: 3.774A pdb=" N LYS B 722 " --> pdb=" O GLY B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 747 removed outlier: 4.173A pdb=" N ARG B 742 " --> pdb=" O ASP B 739 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU B 745 " --> pdb=" O ARG B 742 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE B 747 " --> pdb=" O LEU B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 755 Processing helix chain 'B' and resid 762 through 770 removed outlier: 3.770A pdb=" N VAL B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 285 through 301 removed outlier: 3.618A pdb=" N VAL C 301 " --> pdb=" O TRP C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 327 through 344 Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.876A pdb=" N GLN C 367 " --> pdb=" O THR C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.529A pdb=" N GLU C 390 " --> pdb=" O ASP C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 414 Processing helix chain 'C' and resid 439 through 444 removed outlier: 4.318A pdb=" N VAL C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 484 Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 513 removed outlier: 3.535A pdb=" N LYS C 509 " --> pdb=" O HIS C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 Processing helix chain 'C' and resid 541 through 561 Processing helix chain 'C' and resid 631 through 648 removed outlier: 3.679A pdb=" N GLN C 635 " --> pdb=" O GLY C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 661 Processing helix chain 'C' and resid 677 through 679 No H-bonds generated for 'chain 'C' and resid 677 through 679' Processing helix chain 'C' and resid 680 through 694 Processing helix chain 'C' and resid 718 through 730 removed outlier: 3.753A pdb=" N LYS C 722 " --> pdb=" O GLY C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 747 removed outlier: 4.804A pdb=" N ARG C 742 " --> pdb=" O ASP C 739 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 747 " --> pdb=" O LEU C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 755 Processing helix chain 'C' and resid 762 through 771 removed outlier: 3.840A pdb=" N VAL C 766 " --> pdb=" O ARG C 762 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 260 Processing helix chain 'D' and resid 264 through 280 removed outlier: 3.950A pdb=" N MET D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 Processing helix chain 'D' and resid 313 through 323 Processing helix chain 'D' and resid 327 through 341 Processing helix chain 'D' and resid 362 through 374 removed outlier: 3.624A pdb=" N GLY D 374 " --> pdb=" O ALA D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 405 through 414 removed outlier: 3.575A pdb=" N LYS D 409 " --> pdb=" O LYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 428 removed outlier: 3.546A pdb=" N MET D 428 " --> pdb=" O ILE D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 444 removed outlier: 3.845A pdb=" N ALA D 439 " --> pdb=" O ASP D 435 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 484 removed outlier: 4.045A pdb=" N ARG D 484 " --> pdb=" O PRO D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 512 removed outlier: 3.532A pdb=" N LYS D 509 " --> pdb=" O HIS D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 536 removed outlier: 3.720A pdb=" N ILE D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR D 536 " --> pdb=" O ILE D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 562 removed outlier: 3.529A pdb=" N ASP D 562 " --> pdb=" O ASN D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 648 Processing helix chain 'D' and resid 648 through 653 Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'D' and resid 677 through 679 No H-bonds generated for 'chain 'D' and resid 677 through 679' Processing helix chain 'D' and resid 680 through 694 removed outlier: 3.787A pdb=" N LEU D 692 " --> pdb=" O LEU D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 728 Processing helix chain 'D' and resid 739 through 747 removed outlier: 4.630A pdb=" N ARG D 742 " --> pdb=" O ASP D 739 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU D 745 " --> pdb=" O ARG D 742 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D 747 " --> pdb=" O LEU D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 755 Processing helix chain 'D' and resid 762 through 771 Processing helix chain 'E' and resid 254 through 262 removed outlier: 3.982A pdb=" N ILE E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU E 259 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS E 262 " --> pdb=" O ILE E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 281 Processing helix chain 'E' and resid 285 through 299 Processing helix chain 'E' and resid 313 through 321 Processing helix chain 'E' and resid 327 through 342 Processing helix chain 'E' and resid 362 through 374 removed outlier: 3.709A pdb=" N GLY E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 404 through 414 Processing helix chain 'E' and resid 435 through 443 removed outlier: 3.693A pdb=" N ALA E 439 " --> pdb=" O ASP E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 483 removed outlier: 4.587A pdb=" N ASP E 483 " --> pdb=" O ALA E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 removed outlier: 3.583A pdb=" N LYS E 498 " --> pdb=" O THR E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 512 removed outlier: 3.516A pdb=" N GLU E 512 " --> pdb=" O PRO E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 Processing helix chain 'E' and resid 541 through 563 removed outlier: 3.914A pdb=" N LYS E 563 " --> pdb=" O LEU E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 579 Processing helix chain 'E' and resid 631 through 648 Processing helix chain 'E' and resid 657 through 661 Processing helix chain 'E' and resid 677 through 679 No H-bonds generated for 'chain 'E' and resid 677 through 679' Processing helix chain 'E' and resid 680 through 694 removed outlier: 3.590A pdb=" N THR E 686 " --> pdb=" O ILE E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 718 through 729 removed outlier: 3.957A pdb=" N LYS E 722 " --> pdb=" O GLY E 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 747 removed outlier: 4.351A pdb=" N ARG E 742 " --> pdb=" O ASP E 739 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE E 747 " --> pdb=" O LEU E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 755 removed outlier: 3.567A pdb=" N ILE E 752 " --> pdb=" O PRO E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 771 removed outlier: 3.783A pdb=" N VAL E 766 " --> pdb=" O ARG E 762 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 769 " --> pdb=" O ASP E 765 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 771 " --> pdb=" O LEU E 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 261 removed outlier: 3.776A pdb=" N ALA F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 279 Processing helix chain 'F' and resid 285 through 297 Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 327 through 344 Processing helix chain 'F' and resid 364 through 374 removed outlier: 3.557A pdb=" N GLY F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 414 removed outlier: 3.840A pdb=" N MET F 410 " --> pdb=" O LEU F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 445 removed outlier: 4.363A pdb=" N VAL F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 483 removed outlier: 3.978A pdb=" N ASP F 483 " --> pdb=" O ALA F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 506 removed outlier: 3.567A pdb=" N LEU F 506 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 515 Processing helix chain 'F' and resid 524 through 535 Processing helix chain 'F' and resid 542 through 561 Processing helix chain 'F' and resid 631 through 648 Processing helix chain 'F' and resid 657 through 661 Processing helix chain 'F' and resid 680 through 694 removed outlier: 3.516A pdb=" N MET F 684 " --> pdb=" O ALA F 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 730 removed outlier: 3.662A pdb=" N GLY F 730 " --> pdb=" O ALA F 726 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 747 removed outlier: 4.721A pdb=" N ARG F 742 " --> pdb=" O ASP F 739 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE F 747 " --> pdb=" O LEU F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 755 Processing helix chain 'F' and resid 762 through 771 removed outlier: 3.755A pdb=" N VAL F 766 " --> pdb=" O ARG F 762 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 769 " --> pdb=" O ASP F 765 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU F 771 " --> pdb=" O LEU F 767 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 380 removed outlier: 6.205A pdb=" N GLN A 376 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU A 421 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL A 378 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 469 " --> pdb=" O PRO A 418 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE A 420 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR A 471 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU A 422 " --> pdb=" O THR A 471 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 352 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER A 472 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU A 354 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 351 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE A 488 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS A 353 " --> pdb=" O ILE A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 521 through 523 removed outlier: 6.627A pdb=" N THR A 522 " --> pdb=" O ILE A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 623 through 627 removed outlier: 4.229A pdb=" N LYS A 623 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N GLN A 597 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N MET A 703 " --> pdb=" O GLN A 597 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 599 " --> pdb=" O MET A 703 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 734 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 760 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A 736 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 706 through 707 removed outlier: 3.606A pdb=" N GLU A 706 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 376 through 381 removed outlier: 7.370A pdb=" N VAL B 469 " --> pdb=" O PRO B 418 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE B 420 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR B 471 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 422 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 351 " --> pdb=" O GLU B 486 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE B 488 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N CYS B 353 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'B' and resid 521 through 523 Processing sheet with id=AA8, first strand: chain 'B' and resid 624 through 627 removed outlier: 9.684A pdb=" N GLN B 597 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 9.829A pdb=" N MET B 703 " --> pdb=" O GLN B 597 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 599 " --> pdb=" O MET B 703 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B 702 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL B 734 " --> pdb=" O HIS B 758 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL B 760 " --> pdb=" O VAL B 734 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 736 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 706 through 707 Processing sheet with id=AB1, first strand: chain 'C' and resid 376 through 381 removed outlier: 7.574A pdb=" N VAL C 469 " --> pdb=" O PRO C 418 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE C 420 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR C 471 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU C 422 " --> pdb=" O THR C 471 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 521 through 523 removed outlier: 6.085A pdb=" N THR C 522 " --> pdb=" O ILE C 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 598 through 603 Processing sheet with id=AB4, first strand: chain 'C' and resid 706 through 707 Processing sheet with id=AB5, first strand: chain 'C' and resid 733 through 737 removed outlier: 6.448A pdb=" N VAL C 734 " --> pdb=" O HIS C 758 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL C 760 " --> pdb=" O VAL C 734 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 736 " --> pdb=" O VAL C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 376 through 381 removed outlier: 6.771A pdb=" N GLN D 376 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU D 421 " --> pdb=" O GLN D 376 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL D 378 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASP D 423 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET D 380 " --> pdb=" O ASP D 423 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL D 469 " --> pdb=" O PRO D 418 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE D 420 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR D 471 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU D 422 " --> pdb=" O THR D 471 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE D 351 " --> pdb=" O GLU D 486 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE D 488 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N CYS D 353 " --> pdb=" O ILE D 488 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 521 through 523 removed outlier: 6.632A pdb=" N THR D 522 " --> pdb=" O ILE D 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 624 through 627 removed outlier: 6.575A pdb=" N THR D 625 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL D 701 " --> pdb=" O GLN D 597 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR D 599 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET D 703 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 601 " --> pdb=" O MET D 703 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA D 702 " --> pdb=" O LEU D 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.568A pdb=" N GLU D 706 " --> pdb=" O LEU D 714 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 376 through 381 removed outlier: 6.675A pdb=" N GLN E 376 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU E 421 " --> pdb=" O GLN E 376 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL E 378 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASP E 423 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET E 380 " --> pdb=" O ASP E 423 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL E 469 " --> pdb=" O PRO E 418 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N PHE E 420 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR E 471 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU E 422 " --> pdb=" O THR E 471 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU E 352 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE E 351 " --> pdb=" O GLU E 486 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AC3, first strand: chain 'E' and resid 521 through 523 removed outlier: 6.968A pdb=" N THR E 522 " --> pdb=" O ILE E 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 624 through 627 removed outlier: 6.879A pdb=" N THR E 599 " --> pdb=" O MET E 703 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL E 734 " --> pdb=" O HIS E 758 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL E 760 " --> pdb=" O VAL E 734 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE E 736 " --> pdb=" O VAL E 760 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 706 through 707 Processing sheet with id=AC6, first strand: chain 'F' and resid 376 through 381 removed outlier: 6.522A pdb=" N GLN F 376 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU F 421 " --> pdb=" O GLN F 376 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL F 378 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ASP F 423 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N MET F 380 " --> pdb=" O ASP F 423 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL F 469 " --> pdb=" O PRO F 418 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE F 420 " --> pdb=" O VAL F 469 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N THR F 471 " --> pdb=" O PHE F 420 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU F 422 " --> pdb=" O THR F 471 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU F 352 " --> pdb=" O ALA F 470 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N SER F 472 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU F 354 " --> pdb=" O SER F 472 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 452 through 453 Processing sheet with id=AC8, first strand: chain 'F' and resid 521 through 523 removed outlier: 6.214A pdb=" N THR F 522 " --> pdb=" O ILE F 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 624 through 627 removed outlier: 9.563A pdb=" N GLN F 597 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 9.580A pdb=" N MET F 703 " --> pdb=" O GLN F 597 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR F 599 " --> pdb=" O MET F 703 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL F 734 " --> pdb=" O HIS F 758 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL F 760 " --> pdb=" O VAL F 734 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE F 736 " --> pdb=" O VAL F 760 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 706 through 707 1028 hydrogen bonds defined for protein. 2949 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: 4.53 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4769 1.33 - 1.45: 5039 1.45 - 1.57: 14621 1.57 - 1.69: 26 1.69 - 1.81: 246 Bond restraints: 24701 Sorted by residual: bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.05e+01 bond pdb=" C4 ATP C 801 " pdb=" C5 ATP C 801 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.96e+01 bond pdb=" C4 ATP D 801 " pdb=" C5 ATP D 801 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.48e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.17e+01 ... (remaining 24696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 33049 3.60 - 7.20: 288 7.20 - 10.80: 25 10.80 - 14.40: 3 14.40 - 18.00: 6 Bond angle restraints: 33371 Sorted by residual: angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 121.87 18.00 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 122.25 17.62 1.00e+00 1.00e+00 3.10e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 122.34 17.53 1.00e+00 1.00e+00 3.07e+02 angle pdb=" PB ATP D 801 " pdb=" O3B ATP D 801 " pdb=" PG ATP D 801 " ideal model delta sigma weight residual 139.87 122.75 17.12 1.00e+00 1.00e+00 2.93e+02 angle pdb=" PA ATP D 801 " pdb=" O3A ATP D 801 " pdb=" PB ATP D 801 " ideal model delta sigma weight residual 136.83 121.66 15.17 1.00e+00 1.00e+00 2.30e+02 ... (remaining 33366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.70: 14959 23.70 - 47.40: 353 47.40 - 71.10: 10 71.10 - 94.80: 2 94.80 - 118.50: 1 Dihedral angle restraints: 15325 sinusoidal: 6341 harmonic: 8984 Sorted by residual: dihedral pdb=" C5' ADP E 801 " pdb=" O5' ADP E 801 " pdb=" PA ADP E 801 " pdb=" O2A ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 -178.50 118.50 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" CA LEU A 422 " pdb=" C LEU A 422 " pdb=" N ASP A 423 " pdb=" CA ASP A 423 " ideal model delta harmonic sigma weight residual 180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA VAL E 668 " pdb=" C VAL E 668 " pdb=" N PRO E 669 " pdb=" CA PRO E 669 " ideal model delta harmonic sigma weight residual -180.00 -153.99 -26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 15322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2298 0.045 - 0.090: 1153 0.090 - 0.135: 330 0.135 - 0.181: 67 0.181 - 0.226: 15 Chirality restraints: 3863 Sorted by residual: chirality pdb=" CA VAL F 378 " pdb=" N VAL F 378 " pdb=" C VAL F 378 " pdb=" CB VAL F 378 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL F 581 " pdb=" CA VAL F 581 " pdb=" CG1 VAL F 581 " pdb=" CG2 VAL F 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO F 669 " pdb=" N PRO F 669 " pdb=" C PRO F 669 " pdb=" CB PRO F 669 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 3860 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 689 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C VAL A 689 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL A 689 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 690 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 690 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C SER C 690 " 0.048 2.00e-02 2.50e+03 pdb=" O SER C 690 " -0.018 2.00e-02 2.50e+03 pdb=" N CYS C 691 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 684 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C MET C 684 " -0.047 2.00e-02 2.50e+03 pdb=" O MET C 684 " 0.018 2.00e-02 2.50e+03 pdb=" N CYS C 685 " 0.016 2.00e-02 2.50e+03 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 274 2.64 - 3.20: 20993 3.20 - 3.77: 37303 3.77 - 4.33: 53734 4.33 - 4.90: 86326 Nonbonded interactions: 198630 Sorted by model distance: nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 2.073 2.170 nonbonded pdb=" OG1 THR B 363 " pdb="MG MG B 802 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR A 363 " pdb="MG MG A 802 " model vdw 2.081 2.170 nonbonded pdb=" O3G ATP A 801 " pdb="MG MG A 802 " model vdw 2.097 2.170 nonbonded pdb=" O2G ATP D 801 " pdb="MG MG D 802 " model vdw 2.112 2.170 ... (remaining 198625 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 253 through 383 or resid 395 through 585 or resid 591 thro \ ugh 775)) selection = (chain 'B' and (resid 253 through 383 or resid 395 through 585 or resid 591 thro \ ugh 775)) selection = (chain 'C' and (resid 253 through 383 or resid 395 through 585 or resid 591 thro \ ugh 775)) selection = (chain 'D' and (resid 253 through 383 or resid 395 through 775)) selection = (chain 'E' and (resid 253 through 383 or resid 395 through 585 or resid 591 thro \ ugh 775)) selection = (chain 'F' and (resid 253 through 585 or resid 591 through 775)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.820 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.006 0.078 24701 Z= 0.313 Angle : 0.983 18.001 33371 Z= 0.605 Chirality : 0.057 0.226 3863 Planarity : 0.008 0.065 4272 Dihedral : 9.919 118.500 9539 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 0.42 % Allowed : 3.05 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.12), residues: 3112 helix: -3.11 (0.10), residues: 1343 sheet: -1.47 (0.22), residues: 492 loop : -2.38 (0.14), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 710 TYR 0.022 0.003 TYR C 493 PHE 0.026 0.003 PHE D 420 TRP 0.015 0.002 TRP A 603 HIS 0.011 0.002 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.31 (24701) covalent geometry : angle 0.98315 / 0.61 (33371) hydrogen bonds : bond 0.15870 / 10.42 ( 1028) hydrogen bonds : angle 9.18181 / 6.32 ( 2949) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 613 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ASP cc_start: 0.7794 (p0) cc_final: 0.7567 (p0) REVERT: A 332 ASP cc_start: 0.7265 (m-30) cc_final: 0.7001 (m-30) REVERT: A 408 GLN cc_start: 0.8613 (mt0) cc_final: 0.8287 (mt0) REVERT: B 274 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7754 (tp30) REVERT: B 472 SER cc_start: 0.8867 (p) cc_final: 0.8663 (t) REVERT: C 604 THR cc_start: 0.8401 (p) cc_final: 0.8198 (p) REVERT: C 754 ASP cc_start: 0.7890 (m-30) cc_final: 0.7656 (m-30) REVERT: D 323 ASP cc_start: 0.7524 (p0) cc_final: 0.7244 (p0) REVERT: D 371 LYS cc_start: 0.8552 (tmtp) cc_final: 0.8314 (tttm) REVERT: D 410 MET cc_start: 0.9177 (mmm) cc_final: 0.8786 (mmm) REVERT: D 669 PRO cc_start: 0.8312 (Cg_endo) cc_final: 0.8096 (Cg_exo) REVERT: E 265 LYS cc_start: 0.7351 (mmmt) cc_final: 0.7077 (mmtt) REVERT: E 304 ASN cc_start: 0.7280 (m-40) cc_final: 0.6826 (m110) REVERT: E 388 GLU cc_start: 0.7707 (tt0) cc_final: 0.6793 (pm20) REVERT: E 406 LEU cc_start: 0.7517 (tm) cc_final: 0.7222 (tt) REVERT: E 440 LEU cc_start: 0.7660 (mt) cc_final: 0.7457 (mt) REVERT: E 453 ASN cc_start: 0.7669 (p0) cc_final: 0.7034 (p0) REVERT: E 538 GLU cc_start: 0.5868 (tt0) cc_final: 0.5620 (tt0) REVERT: F 402 MET cc_start: 0.5628 (mmm) cc_final: 0.5189 (ttm) REVERT: F 410 MET cc_start: 0.8701 (mmm) cc_final: 0.8468 (mmt) REVERT: F 487 VAL cc_start: 0.8410 (t) cc_final: 0.8156 (t) outliers start: 11 outliers final: 3 residues processed: 621 average time/residue: 0.8192 time to fit residues: 569.7097 Evaluate side-chains 437 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 434 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain F residue 274 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN A 324 HIS A 341 GLN A 367 GLN A 394 HIS A 448 GLN A 473 ASN A 476 ASN A 510 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN B 455 HIS B 500 ASN B 505 HIS B 558 ASN B 571 ASN C 453 ASN C 476 ASN D 304 ASN D 324 HIS D 449 ASN D 455 HIS D 473 ASN D 773 HIS E 408 GLN E 510 GLN E 655 ASN F 324 HIS F 500 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096687 restraints weight = 38104.916| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.70 r_work: 0.3002 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24701 Z= 0.245 Angle : 0.692 11.335 33371 Z= 0.356 Chirality : 0.049 0.217 3863 Planarity : 0.006 0.056 4272 Dihedral : 6.671 97.309 3427 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.01 % Allowed : 13.11 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.14), residues: 3112 helix: -1.14 (0.13), residues: 1435 sheet: -0.98 (0.23), residues: 481 loop : -1.85 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 333 TYR 0.022 0.002 TYR C 398 PHE 0.018 0.002 PHE B 468 TRP 0.015 0.002 TRP F 603 HIS 0.006 0.002 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.24 (24701) covalent geometry : angle 0.69217 / 0.36 (33371) hydrogen bonds : bond 0.04662 / 3.04 ( 1028) hydrogen bonds : angle 5.37734 / 3.70 ( 2949) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 446 time to evaluate : 1.074 Fit side-chains REVERT: A 265 LYS cc_start: 0.8740 (ptmm) cc_final: 0.8245 (tptt) REVERT: A 268 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7954 (ttm110) REVERT: A 392 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7340 (mtp180) REVERT: A 421 LEU cc_start: 0.8710 (tm) cc_final: 0.8263 (tm) REVERT: A 432 MET cc_start: 0.6640 (mpm) cc_final: 0.5756 (ttp) REVERT: A 460 ASP cc_start: 0.8407 (m-30) cc_final: 0.8175 (m-30) REVERT: A 512 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 660 GLU cc_start: 0.7448 (mp0) cc_final: 0.6511 (mp0) REVERT: B 346 LYS cc_start: 0.8537 (tptp) cc_final: 0.8202 (tptt) REVERT: B 386 ARG cc_start: 0.7892 (ptp-110) cc_final: 0.7621 (ptt-90) REVERT: B 444 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8919 (pp) REVERT: B 460 ASP cc_start: 0.9004 (m-30) cc_final: 0.8725 (m-30) REVERT: B 472 SER cc_start: 0.9173 (p) cc_final: 0.8931 (t) REVERT: C 265 LYS cc_start: 0.9056 (tttm) cc_final: 0.8802 (tttm) REVERT: C 563 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8455 (mttp) REVERT: C 583 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8487 (mptp) REVERT: C 604 THR cc_start: 0.8908 (p) cc_final: 0.8417 (t) REVERT: C 754 ASP cc_start: 0.8319 (m-30) cc_final: 0.8044 (m-30) REVERT: D 410 MET cc_start: 0.9157 (mmm) cc_final: 0.8883 (mmm) REVERT: D 435 ASP cc_start: 0.8254 (p0) cc_final: 0.8046 (p0) REVERT: D 476 ASN cc_start: 0.8414 (t0) cc_final: 0.8015 (t0) REVERT: D 525 ASP cc_start: 0.8221 (m-30) cc_final: 0.7899 (p0) REVERT: E 265 LYS cc_start: 0.7287 (mmmt) cc_final: 0.6630 (tptp) REVERT: E 333 ARG cc_start: 0.7448 (tpp80) cc_final: 0.7101 (tpt170) REVERT: E 388 GLU cc_start: 0.7910 (tt0) cc_final: 0.6798 (pm20) REVERT: E 453 ASN cc_start: 0.7863 (p0) cc_final: 0.7451 (p0) REVERT: E 517 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7586 (mppt) REVERT: E 651 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7341 (pttt) REVERT: F 280 MET cc_start: 0.5486 (mpp) cc_final: 0.4901 (tpt) REVERT: F 513 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8271 (ptp-110) REVERT: F 517 LYS cc_start: 0.8134 (pmtt) cc_final: 0.7877 (pmtt) REVERT: F 746 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7298 (tm-30) outliers start: 79 outliers final: 24 residues processed: 487 average time/residue: 0.7959 time to fit residues: 437.1941 Evaluate side-chains 424 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 393 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 537 ARG Chi-restraints excluded: chain C residue 563 LYS Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 517 LYS Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 513 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 114 optimal weight: 1.9990 chunk 150 optimal weight: 20.0000 chunk 263 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 297 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN A 367 GLN A 476 ASN A 639 GLN B 449 ASN B 473 ASN D 408 GLN D 505 HIS E 408 GLN E 424 GLN E 639 GLN F 449 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.102050 restraints weight = 38122.641| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.70 r_work: 0.3033 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24701 Z= 0.154 Angle : 0.588 7.040 33371 Z= 0.300 Chirality : 0.046 0.199 3863 Planarity : 0.005 0.056 4272 Dihedral : 6.174 93.713 3424 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.01 % Allowed : 14.06 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.15), residues: 3112 helix: -0.11 (0.14), residues: 1432 sheet: -0.69 (0.24), residues: 471 loop : -1.50 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 392 TYR 0.013 0.001 TYR C 398 PHE 0.011 0.001 PHE A 420 TRP 0.017 0.002 TRP B 603 HIS 0.004 0.001 HIS F 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (24701) covalent geometry : angle 0.58793 / 0.30 (33371) hydrogen bonds : bond 0.03548 / 2.31 ( 1028) hydrogen bonds : angle 4.81582 / 3.31 ( 2949) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 446 time to evaluate : 1.007 Fit side-chains REVERT: A 265 LYS cc_start: 0.8584 (ptmm) cc_final: 0.8220 (tptt) REVERT: A 266 ASP cc_start: 0.8099 (p0) cc_final: 0.7722 (p0) REVERT: A 306 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8085 (ttp80) REVERT: A 421 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8275 (tp) REVERT: A 432 MET cc_start: 0.6708 (mpm) cc_final: 0.5864 (ttp) REVERT: A 435 ASP cc_start: 0.8065 (t0) cc_final: 0.7803 (t0) REVERT: A 512 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 518 LYS cc_start: 0.8957 (mppt) cc_final: 0.8721 (mmmm) REVERT: A 592 GLU cc_start: 0.8378 (tt0) cc_final: 0.8130 (tt0) REVERT: A 660 GLU cc_start: 0.7393 (mp0) cc_final: 0.6629 (mp0) REVERT: B 472 SER cc_start: 0.9170 (p) cc_final: 0.8840 (t) REVERT: C 276 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8040 (tp40) REVERT: C 432 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.6139 (pp-130) REVERT: C 604 THR cc_start: 0.8912 (p) cc_final: 0.8491 (t) REVERT: C 754 ASP cc_start: 0.8254 (m-30) cc_final: 0.8004 (m-30) REVERT: D 525 ASP cc_start: 0.8172 (m-30) cc_final: 0.7905 (p0) REVERT: E 265 LYS cc_start: 0.7060 (mmmt) cc_final: 0.6783 (tptp) REVERT: E 284 MET cc_start: 0.5441 (tpp) cc_final: 0.5236 (tpp) REVERT: E 333 ARG cc_start: 0.7284 (tpp80) cc_final: 0.6946 (tpt170) REVERT: E 386 ARG cc_start: 0.6844 (mpp-170) cc_final: 0.6447 (mtm110) REVERT: E 388 GLU cc_start: 0.7873 (tt0) cc_final: 0.6740 (pm20) REVERT: E 453 ASN cc_start: 0.7835 (p0) cc_final: 0.7390 (p0) REVERT: E 485 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8125 (mmm) REVERT: E 605 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7102 (tm-30) REVERT: E 651 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7356 (pttt) REVERT: F 517 LYS cc_start: 0.8134 (pmtt) cc_final: 0.7749 (pmtt) outliers start: 79 outliers final: 34 residues processed: 488 average time/residue: 0.7986 time to fit residues: 438.7071 Evaluate side-chains 426 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 386 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 710 ARG Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 537 ARG Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 31 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 289 optimal weight: 9.9990 chunk 265 optimal weight: 0.9990 chunk 275 optimal weight: 0.3980 chunk 182 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN A 639 GLN B 449 ASN D 341 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099237 restraints weight = 37407.028| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.59 r_work: 0.3070 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24701 Z= 0.128 Angle : 0.562 9.589 33371 Z= 0.283 Chirality : 0.044 0.186 3863 Planarity : 0.004 0.056 4272 Dihedral : 5.874 91.002 3424 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.82 % Allowed : 15.36 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 3112 helix: 0.44 (0.14), residues: 1428 sheet: -0.53 (0.24), residues: 472 loop : -1.31 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 392 TYR 0.015 0.001 TYR A 626 PHE 0.014 0.001 PHE A 420 TRP 0.020 0.001 TRP B 603 HIS 0.003 0.001 HIS E 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (24701) covalent geometry : angle 0.56194 / 0.28 (33371) hydrogen bonds : bond 0.03171 / 2.07 ( 1028) hydrogen bonds : angle 4.58577 / 3.15 ( 2949) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 416 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 ASP cc_start: 0.8093 (p0) cc_final: 0.7777 (p0) REVERT: A 291 VAL cc_start: 0.9002 (m) cc_final: 0.8783 (p) REVERT: A 306 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8051 (ttp80) REVERT: A 392 ARG cc_start: 0.7783 (mtp180) cc_final: 0.7489 (mtp180) REVERT: A 395 ARG cc_start: 0.7606 (mpt90) cc_final: 0.7398 (tpp80) REVERT: A 421 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8360 (tp) REVERT: A 432 MET cc_start: 0.6630 (mpm) cc_final: 0.5848 (ttp) REVERT: A 435 ASP cc_start: 0.8038 (t0) cc_final: 0.7766 (t0) REVERT: A 512 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8287 (tm-30) REVERT: A 592 GLU cc_start: 0.8296 (tt0) cc_final: 0.7985 (tt0) REVERT: A 660 GLU cc_start: 0.7303 (mp0) cc_final: 0.6582 (mp0) REVERT: A 738 ASP cc_start: 0.8576 (t70) cc_final: 0.8339 (t0) REVERT: B 321 ASP cc_start: 0.8821 (m-30) cc_final: 0.8498 (m-30) REVERT: B 346 LYS cc_start: 0.8540 (tptt) cc_final: 0.8338 (tppt) REVERT: B 472 SER cc_start: 0.9120 (p) cc_final: 0.8852 (t) REVERT: B 650 ASP cc_start: 0.8356 (t70) cc_final: 0.8080 (t0) REVERT: B 684 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8023 (mtt) REVERT: C 328 GLU cc_start: 0.8113 (mp0) cc_final: 0.7908 (mm-30) REVERT: C 432 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6178 (pp-130) REVERT: C 476 ASN cc_start: 0.8457 (t0) cc_final: 0.8188 (p0) REVERT: C 604 THR cc_start: 0.8890 (p) cc_final: 0.8475 (t) REVERT: C 754 ASP cc_start: 0.8221 (m-30) cc_final: 0.7985 (m-30) REVERT: E 333 ARG cc_start: 0.7411 (tpp80) cc_final: 0.7163 (tpt170) REVERT: E 386 ARG cc_start: 0.6767 (mpp-170) cc_final: 0.6431 (mtm110) REVERT: E 453 ASN cc_start: 0.8058 (p0) cc_final: 0.7623 (p0) REVERT: E 588 ARG cc_start: 0.8897 (ptp90) cc_final: 0.8664 (ptp90) REVERT: E 605 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7083 (tm-30) REVERT: E 651 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7353 (pttt) REVERT: F 280 MET cc_start: 0.5350 (mpp) cc_final: 0.4652 (tpt) REVERT: F 402 MET cc_start: 0.5865 (mmm) cc_final: 0.5300 (ttp) outliers start: 74 outliers final: 31 residues processed: 462 average time/residue: 0.7638 time to fit residues: 398.4356 Evaluate side-chains 422 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 386 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 634 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 11 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 1 optimal weight: 30.0000 chunk 126 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 449 ASN C 567 HIS E 727 HIS F 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096791 restraints weight = 37583.373| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.62 r_work: 0.3023 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24701 Z= 0.209 Angle : 0.627 9.893 33371 Z= 0.315 Chirality : 0.047 0.198 3863 Planarity : 0.005 0.056 4272 Dihedral : 6.078 91.150 3424 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.35 % Allowed : 15.85 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 3112 helix: 0.58 (0.14), residues: 1426 sheet: -0.38 (0.24), residues: 463 loop : -1.15 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 742 TYR 0.018 0.002 TYR C 398 PHE 0.027 0.002 PHE A 420 TRP 0.021 0.002 TRP B 603 HIS 0.006 0.001 HIS C 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (24701) covalent geometry : angle 0.62709 / 0.32 (33371) hydrogen bonds : bond 0.03747 / 2.45 ( 1028) hydrogen bonds : angle 4.65847 / 3.21 ( 2949) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 408 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 291 VAL cc_start: 0.9012 (m) cc_final: 0.8783 (p) REVERT: A 306 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8171 (ttp80) REVERT: A 392 ARG cc_start: 0.7798 (mtp180) cc_final: 0.7593 (mtp180) REVERT: A 512 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8298 (tm-30) REVERT: A 592 GLU cc_start: 0.8246 (tt0) cc_final: 0.7989 (tt0) REVERT: A 604 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8424 (m) REVERT: A 660 GLU cc_start: 0.7474 (mp0) cc_final: 0.6468 (mp0) REVERT: B 321 ASP cc_start: 0.8858 (m-30) cc_final: 0.8549 (m-30) REVERT: B 346 LYS cc_start: 0.8585 (tptt) cc_final: 0.8371 (tppt) REVERT: B 472 SER cc_start: 0.9103 (p) cc_final: 0.8876 (t) REVERT: B 650 ASP cc_start: 0.8427 (t70) cc_final: 0.8149 (t0) REVERT: B 684 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8104 (mtt) REVERT: C 276 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8017 (tp40) REVERT: C 309 VAL cc_start: 0.9360 (t) cc_final: 0.9084 (m) REVERT: C 328 GLU cc_start: 0.8168 (mp0) cc_final: 0.7960 (mm-30) REVERT: C 476 ASN cc_start: 0.8526 (t0) cc_final: 0.8240 (p0) REVERT: C 583 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8484 (mptp) REVERT: C 604 THR cc_start: 0.8927 (p) cc_final: 0.8550 (t) REVERT: C 754 ASP cc_start: 0.8238 (m-30) cc_final: 0.8004 (m-30) REVERT: D 420 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8703 (t80) REVERT: E 284 MET cc_start: 0.5440 (tpp) cc_final: 0.5150 (tpp) REVERT: E 333 ARG cc_start: 0.7374 (tpp80) cc_final: 0.7102 (tpt170) REVERT: E 396 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.5831 (ptm-80) REVERT: E 420 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: E 453 ASN cc_start: 0.8093 (p0) cc_final: 0.7892 (p0) REVERT: E 537 ARG cc_start: 0.7766 (tpm170) cc_final: 0.7374 (tpp-160) REVERT: E 588 ARG cc_start: 0.8940 (ptp90) cc_final: 0.8734 (ptp90) REVERT: E 605 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6993 (tm-30) REVERT: E 651 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7363 (pttt) REVERT: F 280 MET cc_start: 0.5223 (mpp) cc_final: 0.4395 (tpt) REVERT: F 333 ARG cc_start: 0.7770 (tpt170) cc_final: 0.7277 (tpt170) outliers start: 88 outliers final: 42 residues processed: 463 average time/residue: 0.7791 time to fit residues: 406.7770 Evaluate side-chains 439 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 388 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 396 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 634 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 127 optimal weight: 3.9990 chunk 117 optimal weight: 0.0060 chunk 299 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 222 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 GLN B 449 ASN D 341 GLN E 727 HIS F 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.094120 restraints weight = 37690.938| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.63 r_work: 0.3038 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24701 Z= 0.159 Angle : 0.592 10.032 33371 Z= 0.297 Chirality : 0.046 0.188 3863 Planarity : 0.005 0.055 4272 Dihedral : 5.923 89.166 3424 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.51 % Allowed : 16.77 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3112 helix: 0.77 (0.14), residues: 1421 sheet: -0.22 (0.25), residues: 446 loop : -1.05 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 742 TYR 0.018 0.001 TYR A 626 PHE 0.018 0.001 PHE A 420 TRP 0.023 0.001 TRP B 603 HIS 0.004 0.001 HIS C 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (24701) covalent geometry : angle 0.59151 / 0.30 (33371) hydrogen bonds : bond 0.03321 / 2.17 ( 1028) hydrogen bonds : angle 4.55382 / 3.14 ( 2949) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 402 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 ASP cc_start: 0.8249 (p0) cc_final: 0.8018 (p0) REVERT: A 291 VAL cc_start: 0.8965 (m) cc_final: 0.8759 (p) REVERT: A 392 ARG cc_start: 0.7799 (mtp180) cc_final: 0.7574 (mtp180) REVERT: A 395 ARG cc_start: 0.8250 (tpp80) cc_final: 0.7752 (mpt90) REVERT: A 406 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8831 (mm) REVERT: A 432 MET cc_start: 0.6582 (mpm) cc_final: 0.5830 (ttp) REVERT: A 512 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8320 (tm-30) REVERT: A 592 GLU cc_start: 0.8207 (tt0) cc_final: 0.7925 (tt0) REVERT: A 660 GLU cc_start: 0.7449 (mp0) cc_final: 0.6481 (mp0) REVERT: A 661 LYS cc_start: 0.8772 (pptt) cc_final: 0.8331 (pptt) REVERT: B 321 ASP cc_start: 0.8835 (m-30) cc_final: 0.8528 (m-30) REVERT: B 346 LYS cc_start: 0.8548 (tptt) cc_final: 0.8338 (tppt) REVERT: B 472 SER cc_start: 0.9108 (p) cc_final: 0.8873 (t) REVERT: B 650 ASP cc_start: 0.8377 (t70) cc_final: 0.8116 (t0) REVERT: B 684 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8055 (mtt) REVERT: C 276 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7962 (tp40) REVERT: C 476 ASN cc_start: 0.8528 (t0) cc_final: 0.8229 (p0) REVERT: C 583 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8461 (mptp) REVERT: C 604 THR cc_start: 0.8880 (p) cc_final: 0.8519 (t) REVERT: C 754 ASP cc_start: 0.8189 (m-30) cc_final: 0.7948 (m-30) REVERT: D 420 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8638 (t80) REVERT: E 284 MET cc_start: 0.5487 (tpp) cc_final: 0.5251 (tpp) REVERT: E 333 ARG cc_start: 0.7409 (tpp80) cc_final: 0.7161 (tpt170) REVERT: E 396 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.5770 (ptm-80) REVERT: E 420 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: E 453 ASN cc_start: 0.8098 (p0) cc_final: 0.7672 (p0) REVERT: E 537 ARG cc_start: 0.7804 (tpm170) cc_final: 0.7381 (tpp-160) REVERT: E 588 ARG cc_start: 0.8953 (ptp90) cc_final: 0.8749 (ptp90) REVERT: E 605 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: E 651 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7363 (pttt) REVERT: F 280 MET cc_start: 0.4990 (mpp) cc_final: 0.4190 (tpt) REVERT: F 402 MET cc_start: 0.6063 (mmm) cc_final: 0.5537 (ttp) REVERT: F 513 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8042 (ttm-80) REVERT: F 517 LYS cc_start: 0.8027 (pmtt) cc_final: 0.7798 (pmtt) outliers start: 92 outliers final: 48 residues processed: 462 average time/residue: 0.7948 time to fit residues: 414.4728 Evaluate side-chains 440 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 382 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 396 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 605 GLU Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 639 GLN Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 513 ARG Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 617 CYS Chi-restraints excluded: chain F residue 634 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 69 optimal weight: 20.0000 chunk 238 optimal weight: 0.0270 chunk 65 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 145 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 307 optimal weight: 0.5980 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 ASN A 639 GLN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN D 341 GLN D 455 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095945 restraints weight = 38091.923| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.63 r_work: 0.3057 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24701 Z= 0.102 Angle : 0.548 9.502 33371 Z= 0.274 Chirality : 0.043 0.178 3863 Planarity : 0.004 0.054 4272 Dihedral : 5.615 86.596 3424 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.48 % Allowed : 18.06 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3112 helix: 1.11 (0.15), residues: 1408 sheet: -0.20 (0.25), residues: 454 loop : -0.92 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 742 TYR 0.016 0.001 TYR A 294 PHE 0.009 0.001 PHE A 420 TRP 0.026 0.001 TRP B 603 HIS 0.002 0.001 HIS B 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (24701) covalent geometry : angle 0.54755 / 0.27 (33371) hydrogen bonds : bond 0.02733 / 1.79 ( 1028) hydrogen bonds : angle 4.35645 / 3.01 ( 2949) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 420 time to evaluate : 0.987 Fit side-chains REVERT: A 291 VAL cc_start: 0.8890 (m) cc_final: 0.8661 (p) REVERT: A 306 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8290 (ttp80) REVERT: A 392 ARG cc_start: 0.7744 (mtp180) cc_final: 0.7479 (mtp180) REVERT: A 395 ARG cc_start: 0.8095 (tpp80) cc_final: 0.7615 (mpt90) REVERT: A 425 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8426 (mm) REVERT: A 432 MET cc_start: 0.6545 (mpm) cc_final: 0.5711 (ttp) REVERT: A 435 ASP cc_start: 0.8129 (t0) cc_final: 0.7854 (t70) REVERT: A 512 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8361 (tm-30) REVERT: A 592 GLU cc_start: 0.8316 (tt0) cc_final: 0.7984 (tt0) REVERT: A 660 GLU cc_start: 0.7348 (mp0) cc_final: 0.5635 (tp30) REVERT: A 661 LYS cc_start: 0.8829 (pptt) cc_final: 0.8382 (pptt) REVERT: A 739 ASP cc_start: 0.8326 (p0) cc_final: 0.7962 (m-30) REVERT: B 321 ASP cc_start: 0.8846 (m-30) cc_final: 0.8524 (m-30) REVERT: B 472 SER cc_start: 0.9178 (p) cc_final: 0.8855 (t) REVERT: B 512 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8393 (tm-30) REVERT: B 650 ASP cc_start: 0.8559 (t70) cc_final: 0.8316 (t0) REVERT: B 684 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8066 (mtt) REVERT: C 265 LYS cc_start: 0.8944 (tttp) cc_final: 0.8626 (tmtm) REVERT: C 432 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.5997 (pp-130) REVERT: C 476 ASN cc_start: 0.8446 (t0) cc_final: 0.8138 (p0) REVERT: C 604 THR cc_start: 0.8831 (p) cc_final: 0.8450 (t) REVERT: C 754 ASP cc_start: 0.8027 (m-30) cc_final: 0.7779 (m-30) REVERT: C 769 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8521 (mt) REVERT: D 323 ASP cc_start: 0.7729 (p0) cc_final: 0.7512 (p0) REVERT: D 348 LYS cc_start: 0.8288 (mptp) cc_final: 0.7409 (ptmm) REVERT: D 661 LYS cc_start: 0.9282 (mttm) cc_final: 0.8828 (mtmt) REVERT: E 269 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7597 (mm-30) REVERT: E 284 MET cc_start: 0.5275 (tpp) cc_final: 0.5016 (tpp) REVERT: E 299 LEU cc_start: 0.8639 (mm) cc_final: 0.8058 (mt) REVERT: E 386 ARG cc_start: 0.6719 (mpp-170) cc_final: 0.6228 (mtm110) REVERT: E 420 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: E 423 ASP cc_start: 0.7542 (t70) cc_final: 0.7247 (t70) REVERT: E 453 ASN cc_start: 0.8118 (p0) cc_final: 0.7647 (p0) REVERT: E 537 ARG cc_start: 0.7778 (tpm170) cc_final: 0.7445 (tpp-160) REVERT: E 568 ILE cc_start: 0.8428 (mt) cc_final: 0.8076 (mm) REVERT: E 588 ARG cc_start: 0.8933 (ptp90) cc_final: 0.8726 (ptp90) REVERT: E 605 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6985 (tm-30) REVERT: E 651 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7358 (ptmt) REVERT: F 280 MET cc_start: 0.4553 (mpp) cc_final: 0.3869 (tpt) REVERT: F 333 ARG cc_start: 0.7569 (tpt170) cc_final: 0.7339 (tpt170) REVERT: F 380 MET cc_start: 0.8335 (ttm) cc_final: 0.8053 (ttp) REVERT: F 402 MET cc_start: 0.5995 (mmm) cc_final: 0.5454 (ttp) REVERT: F 513 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8051 (ttm-80) REVERT: F 517 LYS cc_start: 0.7977 (pmtt) cc_final: 0.7698 (pmtt) outliers start: 65 outliers final: 28 residues processed: 460 average time/residue: 0.7790 time to fit residues: 404.5228 Evaluate side-chains 429 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 393 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 525 ASP Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 513 ARG Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 634 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 309 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 292 optimal weight: 20.0000 chunk 242 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 455 HIS E 455 HIS F 449 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.092446 restraints weight = 37736.587| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.56 r_work: 0.2996 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24701 Z= 0.223 Angle : 0.656 10.396 33371 Z= 0.330 Chirality : 0.048 0.242 3863 Planarity : 0.005 0.054 4272 Dihedral : 6.002 89.212 3424 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.78 % Allowed : 18.56 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3112 helix: 0.92 (0.14), residues: 1422 sheet: -0.22 (0.25), residues: 456 loop : -0.89 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 594 TYR 0.025 0.002 TYR A 294 PHE 0.020 0.002 PHE A 420 TRP 0.030 0.002 TRP B 603 HIS 0.006 0.001 HIS C 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.22 (24701) covalent geometry : angle 0.65556 / 0.33 (33371) hydrogen bonds : bond 0.03731 / 2.45 ( 1028) hydrogen bonds : angle 4.58135 / 3.17 ( 2949) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 398 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 VAL cc_start: 0.8985 (m) cc_final: 0.8773 (p) REVERT: A 395 ARG cc_start: 0.8259 (tpp80) cc_final: 0.7757 (mpt90) REVERT: A 402 MET cc_start: 0.8846 (ptm) cc_final: 0.8618 (ptp) REVERT: A 432 MET cc_start: 0.6627 (mpm) cc_final: 0.5680 (ttm) REVERT: A 512 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8351 (tm-30) REVERT: A 592 GLU cc_start: 0.8216 (tt0) cc_final: 0.7935 (tt0) REVERT: A 655 ASN cc_start: 0.8708 (t0) cc_final: 0.8480 (t0) REVERT: B 255 LYS cc_start: 0.7722 (pmtt) cc_final: 0.7302 (ttmm) REVERT: B 279 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6135 (mttt) REVERT: B 321 ASP cc_start: 0.8881 (m-30) cc_final: 0.8588 (m-30) REVERT: B 472 SER cc_start: 0.9076 (p) cc_final: 0.8829 (t) REVERT: B 684 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8167 (mtt) REVERT: C 265 LYS cc_start: 0.9028 (tttp) cc_final: 0.8803 (tmtm) REVERT: C 309 VAL cc_start: 0.9339 (t) cc_final: 0.9060 (m) REVERT: C 476 ASN cc_start: 0.8542 (t0) cc_final: 0.8243 (p0) REVERT: C 604 THR cc_start: 0.8914 (p) cc_final: 0.8568 (t) REVERT: C 605 GLU cc_start: 0.8151 (tp30) cc_final: 0.7923 (tt0) REVERT: D 420 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8654 (t80) REVERT: E 263 MET cc_start: 0.8041 (mtp) cc_final: 0.7723 (mtp) REVERT: E 269 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7732 (mm-30) REVERT: E 284 MET cc_start: 0.5599 (tpp) cc_final: 0.5353 (tpp) REVERT: E 380 MET cc_start: 0.8036 (ttt) cc_final: 0.7719 (ttm) REVERT: E 420 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: E 453 ASN cc_start: 0.8127 (p0) cc_final: 0.7830 (p0) REVERT: E 537 ARG cc_start: 0.7783 (tpm170) cc_final: 0.7263 (tpp-160) REVERT: E 568 ILE cc_start: 0.8490 (mt) cc_final: 0.8128 (mm) REVERT: E 605 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: E 651 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7276 (pttt) REVERT: F 280 MET cc_start: 0.4749 (mpp) cc_final: 0.4168 (tpt) REVERT: F 513 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8108 (ptp-110) REVERT: F 517 LYS cc_start: 0.8062 (pmtt) cc_final: 0.7803 (pmtt) REVERT: F 754 ASP cc_start: 0.8661 (m-30) cc_final: 0.8455 (m-30) outliers start: 73 outliers final: 39 residues processed: 443 average time/residue: 0.7871 time to fit residues: 394.0021 Evaluate side-chains 425 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 379 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 605 GLU Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 513 ARG Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 617 CYS Chi-restraints excluded: chain F residue 634 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 289 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 271 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 GLN D 341 GLN D 455 HIS F 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.092775 restraints weight = 37843.438| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.58 r_work: 0.3001 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24701 Z= 0.196 Angle : 0.643 11.815 33371 Z= 0.322 Chirality : 0.047 0.242 3863 Planarity : 0.005 0.054 4272 Dihedral : 5.975 88.247 3424 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.63 % Allowed : 19.02 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 3112 helix: 1.03 (0.14), residues: 1400 sheet: -0.13 (0.25), residues: 446 loop : -0.86 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 256 TYR 0.013 0.002 TYR A 294 PHE 0.017 0.002 PHE A 420 TRP 0.034 0.002 TRP B 603 HIS 0.005 0.001 HIS C 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (24701) covalent geometry : angle 0.64324 / 0.32 (33371) hydrogen bonds : bond 0.03487 / 2.29 ( 1028) hydrogen bonds : angle 4.57689 / 3.17 ( 2949) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 384 time to evaluate : 0.860 Fit side-chains REVERT: A 257 LYS cc_start: 0.8384 (mptt) cc_final: 0.8177 (mtmm) REVERT: A 306 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8275 (ttp80) REVERT: A 395 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7588 (mpt90) REVERT: A 402 MET cc_start: 0.8809 (ptm) cc_final: 0.8597 (ptp) REVERT: A 432 MET cc_start: 0.6629 (mpm) cc_final: 0.5638 (ttm) REVERT: A 512 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8341 (tm-30) REVERT: A 592 GLU cc_start: 0.8213 (tt0) cc_final: 0.7928 (tt0) REVERT: A 655 ASN cc_start: 0.8727 (t0) cc_final: 0.8434 (t0) REVERT: A 659 TYR cc_start: 0.7856 (t80) cc_final: 0.7317 (t80) REVERT: A 660 GLU cc_start: 0.7392 (mp0) cc_final: 0.6332 (tt0) REVERT: B 255 LYS cc_start: 0.7968 (pmtt) cc_final: 0.7312 (ttmm) REVERT: B 279 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6143 (mttt) REVERT: B 321 ASP cc_start: 0.8899 (m-30) cc_final: 0.8608 (m-30) REVERT: B 472 SER cc_start: 0.9118 (p) cc_final: 0.8838 (t) REVERT: B 684 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8077 (mtt) REVERT: C 265 LYS cc_start: 0.9053 (tttp) cc_final: 0.8792 (tmtm) REVERT: C 309 VAL cc_start: 0.9320 (t) cc_final: 0.9042 (m) REVERT: C 476 ASN cc_start: 0.8495 (t0) cc_final: 0.8159 (p0) REVERT: C 604 THR cc_start: 0.8858 (p) cc_final: 0.8513 (t) REVERT: C 605 GLU cc_start: 0.8189 (tp30) cc_final: 0.7942 (tt0) REVERT: D 347 ILE cc_start: 0.8704 (mt) cc_final: 0.8503 (mp) REVERT: D 538 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6589 (pm20) REVERT: E 263 MET cc_start: 0.8029 (mtp) cc_final: 0.7677 (mtp) REVERT: E 269 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7679 (mm-30) REVERT: E 333 ARG cc_start: 0.7400 (tpp80) cc_final: 0.7050 (tpt170) REVERT: E 380 MET cc_start: 0.7983 (ttt) cc_final: 0.7651 (ttm) REVERT: E 420 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: E 453 ASN cc_start: 0.8072 (p0) cc_final: 0.7808 (p0) REVERT: E 537 ARG cc_start: 0.7803 (tpm170) cc_final: 0.7301 (tpp-160) REVERT: E 568 ILE cc_start: 0.8432 (mt) cc_final: 0.8086 (mm) REVERT: E 588 ARG cc_start: 0.8989 (ptp90) cc_final: 0.8725 (ptt-90) REVERT: E 605 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: E 651 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7251 (pttt) REVERT: F 280 MET cc_start: 0.4716 (mpp) cc_final: 0.4205 (tpt) REVERT: F 513 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8163 (ptp-110) REVERT: F 754 ASP cc_start: 0.8626 (m-30) cc_final: 0.8414 (m-30) outliers start: 69 outliers final: 47 residues processed: 427 average time/residue: 0.7792 time to fit residues: 376.4054 Evaluate side-chains 428 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 373 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 538 GLU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 442 GLU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 605 GLU Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 639 GLN Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 513 ARG Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 617 CYS Chi-restraints excluded: chain F residue 634 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 86 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 301 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 21 optimal weight: 20.0000 chunk 267 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 299 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 GLN D 341 GLN D 455 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.094223 restraints weight = 37875.995| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.64 r_work: 0.3025 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24701 Z= 0.125 Angle : 0.600 12.767 33371 Z= 0.301 Chirality : 0.045 0.219 3863 Planarity : 0.004 0.054 4272 Dihedral : 5.731 86.745 3424 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.02 % Allowed : 19.86 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 3112 helix: 1.23 (0.15), residues: 1399 sheet: -0.02 (0.25), residues: 444 loop : -0.77 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 256 TYR 0.015 0.001 TYR A 294 PHE 0.010 0.001 PHE A 420 TRP 0.036 0.002 TRP B 603 HIS 0.003 0.001 HIS C 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 (24701) covalent geometry : angle 0.60037 / 0.30 (33371) hydrogen bonds : bond 0.02974 / 1.95 ( 1028) hydrogen bonds : angle 4.46395 / 3.09 ( 2949) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 391 time to evaluate : 0.840 Fit side-chains REVERT: A 392 ARG cc_start: 0.7599 (mtp180) cc_final: 0.7228 (ptt90) REVERT: A 395 ARG cc_start: 0.7942 (tpp80) cc_final: 0.7450 (mpt90) REVERT: A 402 MET cc_start: 0.8773 (ptm) cc_final: 0.8560 (ptp) REVERT: A 432 MET cc_start: 0.6570 (mpm) cc_final: 0.5676 (ttm) REVERT: A 435 ASP cc_start: 0.8139 (t0) cc_final: 0.7868 (t70) REVERT: A 512 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8356 (tm-30) REVERT: A 592 GLU cc_start: 0.8276 (tt0) cc_final: 0.7925 (tt0) REVERT: A 655 ASN cc_start: 0.8747 (t0) cc_final: 0.8493 (t0) REVERT: A 660 GLU cc_start: 0.7292 (mp0) cc_final: 0.6179 (tt0) REVERT: B 255 LYS cc_start: 0.8052 (pmtt) cc_final: 0.7471 (ttmm) REVERT: B 279 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6312 (mttt) REVERT: B 321 ASP cc_start: 0.8886 (m-30) cc_final: 0.8560 (m-30) REVERT: B 461 TYR cc_start: 0.8899 (t80) cc_final: 0.8483 (t80) REVERT: B 472 SER cc_start: 0.9140 (p) cc_final: 0.8843 (t) REVERT: B 512 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 650 ASP cc_start: 0.8580 (t70) cc_final: 0.8351 (t0) REVERT: B 684 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8025 (mtt) REVERT: C 265 LYS cc_start: 0.8963 (tttp) cc_final: 0.8683 (tmtm) REVERT: C 328 GLU cc_start: 0.8092 (mp0) cc_final: 0.7881 (mm-30) REVERT: C 476 ASN cc_start: 0.8451 (t0) cc_final: 0.8139 (p0) REVERT: C 583 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8437 (mptp) REVERT: C 604 THR cc_start: 0.8822 (p) cc_final: 0.8446 (t) REVERT: C 605 GLU cc_start: 0.8248 (tp30) cc_final: 0.7968 (tt0) REVERT: D 348 LYS cc_start: 0.8260 (mptp) cc_final: 0.7422 (ptmm) REVERT: E 263 MET cc_start: 0.7973 (mtp) cc_final: 0.7694 (mtp) REVERT: E 269 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7681 (mm-30) REVERT: E 281 MET cc_start: 0.3845 (ptp) cc_final: 0.2930 (pmm) REVERT: E 284 MET cc_start: 0.5194 (tmm) cc_final: 0.4764 (tpp) REVERT: E 380 MET cc_start: 0.7974 (ttt) cc_final: 0.7633 (ttm) REVERT: E 420 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: E 453 ASN cc_start: 0.8158 (p0) cc_final: 0.7895 (p0) REVERT: E 458 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7714 (mt-10) REVERT: E 537 ARG cc_start: 0.7790 (tpm170) cc_final: 0.7303 (tpp-160) REVERT: E 568 ILE cc_start: 0.8455 (mt) cc_final: 0.8104 (mm) REVERT: E 588 ARG cc_start: 0.8974 (ptp90) cc_final: 0.8716 (ptt-90) REVERT: E 605 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: E 651 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7316 (ptmt) REVERT: F 280 MET cc_start: 0.4520 (mpp) cc_final: 0.3925 (tpt) REVERT: F 380 MET cc_start: 0.8287 (ttm) cc_final: 0.8086 (ttp) REVERT: F 402 MET cc_start: 0.6063 (mmm) cc_final: 0.5523 (ttp) REVERT: F 513 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8077 (ttm-80) REVERT: F 517 LYS cc_start: 0.8106 (pmmt) cc_final: 0.7795 (pmtt) REVERT: F 754 ASP cc_start: 0.8547 (m-30) cc_final: 0.8328 (m-30) outliers start: 53 outliers final: 33 residues processed: 423 average time/residue: 0.7970 time to fit residues: 379.9714 Evaluate side-chains 422 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 382 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 605 GLU Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 513 ARG Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 634 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 305 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 GLN D 455 HIS D 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.093962 restraints weight = 38106.203| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.65 r_work: 0.3024 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24701 Z= 0.140 Angle : 0.606 11.202 33371 Z= 0.304 Chirality : 0.045 0.216 3863 Planarity : 0.004 0.054 4272 Dihedral : 5.739 86.586 3424 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.91 % Allowed : 19.93 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 3112 helix: 1.26 (0.15), residues: 1396 sheet: 0.06 (0.25), residues: 441 loop : -0.74 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 256 TYR 0.024 0.001 TYR A 626 PHE 0.012 0.001 PHE A 420 TRP 0.036 0.002 TRP B 603 HIS 0.003 0.001 HIS D 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (24701) covalent geometry : angle 0.60553 / 0.30 (33371) hydrogen bonds : bond 0.03076 / 2.02 ( 1028) hydrogen bonds : angle 4.44415 / 3.08 ( 2949) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8849.41 seconds wall clock time: 151 minutes 42.18 seconds (9102.18 seconds total)