Starting phenix.real_space_refine on Tue Jan 21 10:47:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yzi_39694/01_2025/8yzi_39694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yzi_39694/01_2025/8yzi_39694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yzi_39694/01_2025/8yzi_39694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yzi_39694/01_2025/8yzi_39694.map" model { file = "/net/cci-nas-00/data/ceres_data/8yzi_39694/01_2025/8yzi_39694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yzi_39694/01_2025/8yzi_39694.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 68 5.16 5 C 10642 2.51 5 N 2750 2.21 5 O 3237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16699 Number of models: 1 Model: "" Number of chains: 18 Chain: "C" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 898 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain: "A" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 898 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain: "B" Number of atoms: 7263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 7263 Classifications: {'peptide': 900} Link IDs: {'PTRANS': 43, 'TRANS': 856} Chain: "D" Number of atoms: 7263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 7263 Classifications: {'peptide': 900} Link IDs: {'PTRANS': 43, 'TRANS': 856} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.12, per 1000 atoms: 0.67 Number of scatterers: 16699 At special positions: 0 Unit cell: (111.09, 126.27, 142.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 68 16.00 O 3237 8.00 N 2750 7.00 C 10642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 378 " distance=2.03 Simple disulfide: pdb=" SG CYS C 361 " - pdb=" SG CYS C 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 769 " - pdb=" SG CYS B 776 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 842 " distance=2.04 Simple disulfide: pdb=" SG CYS D 769 " - pdb=" SG CYS D 776 " distance=2.03 Simple disulfide: pdb=" SG CYS D 806 " - pdb=" SG CYS D 842 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 501 " - " ASN A 311 " " NAG B1001 " - " ASN B 134 " " NAG B1002 " - " ASN B 271 " " NAG B1003 " - " ASN B 826 " " NAG C 501 " - " ASN C 311 " " NAG D1001 " - " ASN D 134 " " NAG D1002 " - " ASN D 271 " " NAG E 1 " - " ASN B 92 " " NAG F 1 " - " ASN B 240 " " NAG G 1 " - " ASN B 633 " " NAG H 1 " - " ASN B 689 " " NAG I 1 " - " ASN B 533 " " NAG J 1 " - " ASN D 92 " " NAG K 1 " - " ASN D 240 " " NAG L 1 " - " ASN D 633 " " NAG M 1 " - " ASN D 689 " " NAG N 1 " - " ASN D 533 " Time building additional restraints: 4.70 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1004 " pdb="ZN ZN B1004 " - pdb=" NE2 HIS B 398 " pdb="ZN ZN B1004 " - pdb=" NE2 HIS B 394 " pdb=" ZN D1003 " pdb="ZN ZN D1003 " - pdb=" NE2 HIS D 398 " pdb="ZN ZN D1003 " - pdb=" NE2 HIS D 394 " 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3884 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 24 sheets defined 46.5% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.992A pdb=" N ASN C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.441A pdb=" N ASN A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 371 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 79 Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.752A pdb=" N LEU B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 286 " --> pdb=" O THR B 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 286' Processing helix chain 'B' and resid 311 through 317 removed outlier: 3.760A pdb=" N GLN B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 338 removed outlier: 4.447A pdb=" N GLY B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 381 through 401 removed outlier: 3.823A pdb=" N GLN B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 412 Processing helix chain 'B' and resid 413 through 432 removed outlier: 5.200A pdb=" N PHE B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 439 removed outlier: 3.588A pdb=" N ASN B 436 " --> pdb=" O PRO B 433 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 437 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS B 438 " --> pdb=" O TRP B 435 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 439 " --> pdb=" O ASN B 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 433 through 439' Processing helix chain 'B' and resid 440 through 450 removed outlier: 4.533A pdb=" N TYR B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ARG B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 477 Processing helix chain 'B' and resid 479 through 497 removed outlier: 3.679A pdb=" N TYR B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 513 Processing helix chain 'B' and resid 519 through 534 removed outlier: 3.851A pdb=" N LEU B 523 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 553 removed outlier: 4.244A pdb=" N ARG B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TRP B 550 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN B 553 " --> pdb=" O ARG B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 621 removed outlier: 3.562A pdb=" N LYS B 621 " --> pdb=" O ASP B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 632 through 635 Processing helix chain 'B' and resid 643 through 657 Processing helix chain 'B' and resid 662 through 679 removed outlier: 3.633A pdb=" N ALA B 667 " --> pdb=" O VAL B 663 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 670 " --> pdb=" O ARG B 666 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 679 " --> pdb=" O ASP B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 690 removed outlier: 3.678A pdb=" N ALA B 687 " --> pdb=" O PRO B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 697 removed outlier: 3.702A pdb=" N LEU B 694 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN B 695 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 697 " --> pdb=" O LEU B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 717 removed outlier: 4.354A pdb=" N TYR B 712 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 746 removed outlier: 3.560A pdb=" N MET B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 727 " --> pdb=" O TYR B 723 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 728 " --> pdb=" O GLY B 724 " (cutoff:3.500A) Proline residue: B 736 - end of helix Processing helix chain 'B' and resid 754 through 772 Processing helix chain 'B' and resid 773 through 789 removed outlier: 3.681A pdb=" N LYS B 789 " --> pdb=" O ALA B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 799 No H-bonds generated for 'chain 'B' and resid 797 through 799' Processing helix chain 'B' and resid 800 through 812 removed outlier: 4.000A pdb=" N CYS B 806 " --> pdb=" O SER B 802 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B 807 " --> pdb=" O THR B 803 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 811 " --> pdb=" O ASN B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 827 Processing helix chain 'B' and resid 829 through 841 removed outlier: 3.942A pdb=" N ALA B 841 " --> pdb=" O ARG B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 856 removed outlier: 3.624A pdb=" N THR B 856 " --> pdb=" O TYR B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 874 Processing helix chain 'B' and resid 875 through 877 No H-bonds generated for 'chain 'B' and resid 875 through 877' Processing helix chain 'B' and resid 879 through 891 removed outlier: 4.418A pdb=" N LEU B 883 " --> pdb=" O ILE B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 900 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 938 through 940 No H-bonds generated for 'chain 'B' and resid 938 through 940' Processing helix chain 'B' and resid 941 through 961 removed outlier: 3.534A pdb=" N GLU B 946 " --> pdb=" O THR B 942 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS B 953 " --> pdb=" O LEU B 949 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 954 " --> pdb=" O GLU B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 973 Processing helix chain 'D' and resid 75 through 79 Processing helix chain 'D' and resid 282 through 286 removed outlier: 3.780A pdb=" N LEU D 285 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU D 286 " --> pdb=" O THR D 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 282 through 286' Processing helix chain 'D' and resid 311 through 317 removed outlier: 3.556A pdb=" N GLN D 317 " --> pdb=" O SER D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 339 removed outlier: 4.398A pdb=" N GLY D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Proline residue: D 329 - end of helix Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.702A pdb=" N LEU D 374 " --> pdb=" O GLU D 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 374' Processing helix chain 'D' and resid 381 through 398 removed outlier: 3.538A pdb=" N LYS D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS D 398 " --> pdb=" O HIS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 412 Processing helix chain 'D' and resid 413 through 432 removed outlier: 5.099A pdb=" N PHE D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU D 426 " --> pdb=" O TYR D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 439 removed outlier: 3.880A pdb=" N ASN D 436 " --> pdb=" O PRO D 433 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU D 437 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LYS D 438 " --> pdb=" O TRP D 435 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP D 439 " --> pdb=" O ASN D 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 433 through 439' Processing helix chain 'D' and resid 440 through 454 removed outlier: 4.592A pdb=" N TYR D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ARG D 448 " --> pdb=" O ASN D 444 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL D 452 " --> pdb=" O ARG D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 468 removed outlier: 3.513A pdb=" N VAL D 468 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 477 removed outlier: 3.564A pdb=" N VAL D 477 " --> pdb=" O GLN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 497 removed outlier: 3.599A pdb=" N TYR D 483 " --> pdb=" O ASP D 479 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY D 486 " --> pdb=" O SER D 482 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA D 487 " --> pdb=" O TYR D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 513 Processing helix chain 'D' and resid 519 through 535 removed outlier: 3.876A pdb=" N LEU D 523 " --> pdb=" O ILE D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 552 removed outlier: 4.120A pdb=" N ARG D 549 " --> pdb=" O ALA D 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TRP D 550 " --> pdb=" O ILE D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 621 removed outlier: 3.659A pdb=" N LYS D 621 " --> pdb=" O ASP D 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 618 through 621' Processing helix chain 'D' and resid 632 through 635 Processing helix chain 'D' and resid 643 through 657 Processing helix chain 'D' and resid 662 through 679 removed outlier: 3.551A pdb=" N ALA D 679 " --> pdb=" O ASP D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 690 removed outlier: 4.137A pdb=" N ALA D 687 " --> pdb=" O PRO D 683 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 688 " --> pdb=" O VAL D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 692 No H-bonds generated for 'chain 'D' and resid 691 through 692' Processing helix chain 'D' and resid 693 through 697 removed outlier: 3.550A pdb=" N GLU D 697 " --> pdb=" O LEU D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 717 removed outlier: 4.194A pdb=" N TRP D 703 " --> pdb=" O GLU D 699 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR D 712 " --> pdb=" O SER D 708 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 745 Proline residue: D 736 - end of helix Processing helix chain 'D' and resid 754 through 771 Processing helix chain 'D' and resid 773 through 790 removed outlier: 3.530A pdb=" N ASN D 790 " --> pdb=" O GLU D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 799 No H-bonds generated for 'chain 'D' and resid 797 through 799' Processing helix chain 'D' and resid 800 through 811 removed outlier: 4.001A pdb=" N CYS D 806 " --> pdb=" O SER D 802 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN D 807 " --> pdb=" O THR D 803 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN D 811 " --> pdb=" O ASN D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 827 Processing helix chain 'D' and resid 829 through 841 removed outlier: 3.911A pdb=" N ALA D 841 " --> pdb=" O ARG D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 855 Processing helix chain 'D' and resid 856 through 858 No H-bonds generated for 'chain 'D' and resid 856 through 858' Processing helix chain 'D' and resid 866 through 877 removed outlier: 3.638A pdb=" N ASN D 877 " --> pdb=" O SER D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 891 removed outlier: 4.368A pdb=" N LEU D 883 " --> pdb=" O ILE D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 899 removed outlier: 4.093A pdb=" N LEU D 895 " --> pdb=" O ASN D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 914 Processing helix chain 'D' and resid 919 through 933 Processing helix chain 'D' and resid 938 through 940 No H-bonds generated for 'chain 'D' and resid 938 through 940' Processing helix chain 'D' and resid 941 through 974 removed outlier: 3.611A pdb=" N GLU D 946 " --> pdb=" O THR D 942 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS D 957 " --> pdb=" O LYS D 953 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLU D 964 " --> pdb=" O LYS D 960 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA D 965 " --> pdb=" O GLU D 961 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 321 through 328 removed outlier: 6.804A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU C 306 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU C 344 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 308 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASN C 346 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 310 " --> pdb=" O ASN C 346 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE C 341 " --> pdb=" O THR C 415 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 404 " --> pdb=" O MET C 388 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS C 389 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 357 " --> pdb=" O LYS C 389 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 333 through 336 removed outlier: 4.640A pdb=" N PHE C 377 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N GLN C 376 " --> pdb=" O GLN C 412 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N GLN C 412 " --> pdb=" O GLN C 376 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N CYS C 378 " --> pdb=" O GLU C 410 " (cutoff:3.500A) removed outlier: 11.503A pdb=" N GLU C 410 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 11.612A pdb=" N SER C 380 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N ALA C 408 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 404 " --> pdb=" O MET C 388 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 328 removed outlier: 3.560A pdb=" N GLU A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 308 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 314 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N MET A 316 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A 341 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 335 removed outlier: 4.825A pdb=" N GLY A 411 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 376 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 409 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AA6, first strand: chain 'B' and resid 134 through 135 removed outlier: 4.236A pdb=" N SER B 180 " --> pdb=" O CYS B 119 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS B 119 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 111 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N THR B 118 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ASN B 240 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR B 91 " --> pdb=" O ASN B 240 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N THR B 242 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 93 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ILE B 244 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 95 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 262 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 125 through 129 Processing sheet with id=AA8, first strand: chain 'B' and resid 198 through 206 removed outlier: 3.727A pdb=" N ALA B 214 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 294 through 299 removed outlier: 8.209A pdb=" N VAL B 366 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP B 348 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR B 368 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE B 350 " --> pdb=" O TYR B 368 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 405 through 407 Processing sheet with id=AB2, first strand: chain 'B' and resid 614 through 616 removed outlier: 3.533A pdb=" N THR B 567 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 593 through 595 removed outlier: 3.605A pdb=" N ILE B 593 " --> pdb=" O MET B 609 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 602 through 603 Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.647A pdb=" N GLN D 181 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 135 removed outlier: 7.647A pdb=" N THR D 108 " --> pdb=" O PRO D 97 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS D 110 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU D 95 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER D 112 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL D 93 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR D 114 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR D 91 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG D 116 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 87 " --> pdb=" O THR D 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 125 through 129 removed outlier: 6.818A pdb=" N TYR D 167 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU D 161 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL D 169 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR D 159 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N HIS D 171 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 198 through 200 Processing sheet with id=AB9, first strand: chain 'D' and resid 203 through 206 Processing sheet with id=AC1, first strand: chain 'D' and resid 250 through 252 Processing sheet with id=AC2, first strand: chain 'D' and resid 294 through 299 removed outlier: 3.533A pdb=" N LYS D 294 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 310 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG D 307 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N VAL D 366 " --> pdb=" O LYS D 346 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP D 348 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N TYR D 368 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 350 " --> pdb=" O TYR D 368 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 367 " --> pdb=" O MET D 360 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 405 through 407 removed outlier: 6.652A pdb=" N THR D 406 " --> pdb=" O THR D 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 614 through 616 removed outlier: 3.506A pdb=" N VAL D 615 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR D 567 " --> pdb=" O ASP D 562 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASN D 641 " --> pdb=" O PRO D 557 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL D 559 " --> pdb=" O ASN D 641 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 593 through 595 Processing sheet with id=AC6, first strand: chain 'D' and resid 602 through 603 747 hydrogen bonds defined for protein. 2088 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: 6.56 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5304 1.34 - 1.46: 4328 1.46 - 1.59: 7371 1.59 - 1.71: 0 1.71 - 1.83: 112 Bond restraints: 17115 Sorted by residual: bond pdb=" CA GLN B 219 " pdb=" C GLN B 219 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.27e-02 6.20e+03 6.42e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.367 0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" CA ALA D 223 " pdb=" C ALA D 223 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.32e-02 5.74e+03 3.78e+00 bond pdb=" CA ALA B 220 " pdb=" C ALA B 220 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.34e-02 5.57e+03 3.32e+00 ... (remaining 17110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 22803 1.84 - 3.68: 454 3.68 - 5.51: 58 5.51 - 7.35: 11 7.35 - 9.19: 3 Bond angle restraints: 23329 Sorted by residual: angle pdb=" N GLN B 219 " pdb=" CA GLN B 219 " pdb=" C GLN B 219 " ideal model delta sigma weight residual 111.07 119.32 -8.25 1.07e+00 8.73e-01 5.94e+01 angle pdb=" N VAL C 395 " pdb=" CA VAL C 395 " pdb=" C VAL C 395 " ideal model delta sigma weight residual 112.12 106.91 5.21 8.40e-01 1.42e+00 3.85e+01 angle pdb=" N GLN D 219 " pdb=" CA GLN D 219 " pdb=" C GLN D 219 " ideal model delta sigma weight residual 111.07 117.62 -6.55 1.07e+00 8.73e-01 3.75e+01 angle pdb=" C PHE D 587 " pdb=" N ASN D 588 " pdb=" CA ASN D 588 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" N GLN D 911 " pdb=" CA GLN D 911 " pdb=" CB GLN D 911 " ideal model delta sigma weight residual 110.28 115.04 -4.76 1.55e+00 4.16e-01 9.43e+00 ... (remaining 23324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 9771 21.45 - 42.90: 581 42.90 - 64.35: 73 64.35 - 85.80: 41 85.80 - 107.25: 11 Dihedral angle restraints: 10477 sinusoidal: 4475 harmonic: 6002 Sorted by residual: dihedral pdb=" CB CYS D 806 " pdb=" SG CYS D 806 " pdb=" SG CYS D 842 " pdb=" CB CYS D 842 " ideal model delta sinusoidal sigma weight residual -86.00 -21.60 -64.40 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CA PHE B 906 " pdb=" C PHE B 906 " pdb=" N SER B 907 " pdb=" CA SER B 907 " ideal model delta harmonic sigma weight residual 180.00 154.36 25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASN D 92 " pdb=" C ASN D 92 " pdb=" N VAL D 93 " pdb=" CA VAL D 93 " ideal model delta harmonic sigma weight residual -180.00 -158.74 -21.26 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 10474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 2668 0.182 - 0.363: 5 0.363 - 0.545: 0 0.545 - 0.726: 2 0.726 - 0.908: 2 Chirality restraints: 2677 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN D 92 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 92 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 689 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 2674 not shown) Planarity restraints: 2963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 92 " 0.027 2.00e-02 2.50e+03 2.58e-02 8.34e+00 pdb=" CG ASN D 92 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN D 92 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN D 92 " -0.028 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 689 " -0.023 2.00e-02 2.50e+03 2.26e-02 6.39e+00 pdb=" CG ASN B 689 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 689 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 689 " 0.030 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 194 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" C ASP B 194 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP B 194 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP B 195 " 0.013 2.00e-02 2.50e+03 ... (remaining 2960 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2630 2.77 - 3.30: 15464 3.30 - 3.83: 26606 3.83 - 4.37: 30267 4.37 - 4.90: 54402 Nonbonded interactions: 129369 Sorted by model distance: nonbonded pdb=" ND2 ASN B 411 " pdb=" O SER B 463 " model vdw 2.232 3.120 nonbonded pdb=" O4 NAG M 2 " pdb=" O7 NAG M 2 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP B 562 " pdb=" OG1 THR B 564 " model vdw 2.246 3.040 nonbonded pdb=" OE1 GLU B 386 " pdb=" OH TYR B 759 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP C 359 " pdb=" NZ LYS C 389 " model vdw 2.252 3.120 ... (remaining 129364 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' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 75 through 974 or resid 1001 through 1002)) selection = (chain 'D' and (resid 75 through 974 or resid 1001 through 1002)) } ncs_group { reference = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) } 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.120 Set scattering table: 0.200 Process input model: 44.450 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17115 Z= 0.207 Angle : 0.607 9.189 23329 Z= 0.321 Chirality : 0.053 0.908 2677 Planarity : 0.004 0.046 2946 Dihedral : 14.396 107.252 6569 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.17 % Allowed : 0.44 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2022 helix: 1.49 (0.19), residues: 780 sheet: 0.65 (0.27), residues: 410 loop : -1.24 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 524 HIS 0.004 0.001 HIS D 740 PHE 0.021 0.001 PHE D 496 TYR 0.019 0.001 TYR D 167 ARG 0.003 0.000 ARG D 788 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 2.788 Fit side-chains revert: symmetry clash REVERT: C 364 ASP cc_start: 0.8226 (p0) cc_final: 0.7883 (p0) REVERT: A 374 PHE cc_start: 0.7948 (m-80) cc_final: 0.7688 (m-80) outliers start: 3 outliers final: 0 residues processed: 159 average time/residue: 0.3071 time to fit residues: 74.3242 Evaluate side-chains 97 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 309 GLN C 414 HIS B 219 GLN B 516 GLN B 763 ASN D 181 GLN D 217 GLN D 219 GLN D 526 HIS D 671 HIS D 973 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.043432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.032450 restraints weight = 89054.663| |-----------------------------------------------------------------------------| r_work (start): 0.2623 rms_B_bonded: 4.02 r_work: 0.2491 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.123 17115 Z= 0.589 Angle : 0.798 8.882 23329 Z= 0.410 Chirality : 0.052 0.434 2677 Planarity : 0.005 0.046 2946 Dihedral : 7.691 57.170 2759 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.43 % Allowed : 6.62 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 2022 helix: 1.29 (0.19), residues: 794 sheet: 0.16 (0.26), residues: 402 loop : -1.26 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 847 HIS 0.008 0.002 HIS B 526 PHE 0.026 0.002 PHE B 496 TYR 0.023 0.002 TYR A 334 ARG 0.005 0.001 ARG D 788 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: C 316 MET cc_start: 0.8944 (mmm) cc_final: 0.8703 (mmm) REVERT: C 357 ARG cc_start: 0.8983 (ptm-80) cc_final: 0.8368 (ptt180) REVERT: C 364 ASP cc_start: 0.8122 (p0) cc_final: 0.7912 (p0) REVERT: A 372 MET cc_start: 0.9115 (pmm) cc_final: 0.8701 (pmm) REVERT: A 387 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8693 (mm-30) REVERT: D 716 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.9016 (mmt) outliers start: 26 outliers final: 18 residues processed: 106 average time/residue: 0.2825 time to fit residues: 48.2036 Evaluate side-chains 109 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 906 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 83 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 4 optimal weight: 40.0000 chunk 66 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 645 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.045324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.034409 restraints weight = 87344.552| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 4.02 r_work: 0.2563 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17115 Z= 0.159 Angle : 0.560 7.317 23329 Z= 0.289 Chirality : 0.044 0.344 2677 Planarity : 0.004 0.045 2946 Dihedral : 6.346 55.001 2759 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.32 % Allowed : 8.89 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 2022 helix: 1.70 (0.19), residues: 796 sheet: 0.33 (0.26), residues: 402 loop : -1.27 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 892 HIS 0.004 0.001 HIS B 394 PHE 0.020 0.001 PHE D 496 TYR 0.012 0.001 TYR B 509 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.957 Fit side-chains REVERT: C 316 MET cc_start: 0.8866 (mmm) cc_final: 0.8459 (mmm) REVERT: C 338 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7364 (ttmt) REVERT: C 357 ARG cc_start: 0.9035 (ptm-80) cc_final: 0.8380 (ptt180) REVERT: A 316 MET cc_start: 0.8402 (mmm) cc_final: 0.8020 (mmm) REVERT: A 357 ARG cc_start: 0.8942 (ttm-80) cc_final: 0.8535 (ttm-80) REVERT: A 364 ASP cc_start: 0.9176 (t0) cc_final: 0.8761 (p0) REVERT: A 372 MET cc_start: 0.9125 (pmm) cc_final: 0.8790 (pmm) REVERT: A 387 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8615 (mt-10) REVERT: A 388 MET cc_start: 0.8645 (mmp) cc_final: 0.8230 (tpp) REVERT: B 568 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9143 (pp) outliers start: 24 outliers final: 13 residues processed: 112 average time/residue: 0.2782 time to fit residues: 50.2097 Evaluate side-chains 103 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 914 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 151 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 84 optimal weight: 0.0370 chunk 200 optimal weight: 4.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN B 570 GLN B 924 GLN D 78 ASN D 644 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.042783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.031741 restraints weight = 88005.500| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 4.04 r_work: 0.2463 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 17115 Z= 0.437 Angle : 0.679 19.715 23329 Z= 0.351 Chirality : 0.048 0.347 2677 Planarity : 0.004 0.045 2946 Dihedral : 6.406 55.486 2759 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.37 % Allowed : 9.33 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 2022 helix: 1.60 (0.19), residues: 798 sheet: 0.05 (0.26), residues: 414 loop : -1.21 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 892 HIS 0.006 0.001 HIS D 319 PHE 0.023 0.002 PHE A 374 TYR 0.021 0.002 TYR B 509 ARG 0.005 0.000 ARG D 788 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 1.997 Fit side-chains REVERT: C 316 MET cc_start: 0.8724 (mmm) cc_final: 0.8170 (mmm) REVERT: C 357 ARG cc_start: 0.8997 (ptm-80) cc_final: 0.8350 (ptt180) REVERT: A 338 LYS cc_start: 0.9071 (mppt) cc_final: 0.8806 (mppt) REVERT: A 364 ASP cc_start: 0.9212 (OUTLIER) cc_final: 0.8908 (t0) REVERT: B 568 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9160 (pp) outliers start: 43 outliers final: 25 residues processed: 118 average time/residue: 0.2740 time to fit residues: 52.2817 Evaluate side-chains 109 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 914 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 947 GLN ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.044540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.033497 restraints weight = 87081.577| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 4.07 r_work: 0.2538 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17115 Z= 0.147 Angle : 0.570 19.306 23329 Z= 0.288 Chirality : 0.044 0.331 2677 Planarity : 0.004 0.046 2946 Dihedral : 5.887 52.681 2759 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.77 % Allowed : 10.82 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 2022 helix: 1.89 (0.19), residues: 790 sheet: 0.24 (0.26), residues: 402 loop : -1.27 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 787 HIS 0.005 0.001 HIS B 394 PHE 0.019 0.001 PHE D 496 TYR 0.012 0.001 TYR D 167 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.918 Fit side-chains revert: symmetry clash REVERT: C 316 MET cc_start: 0.8758 (mmm) cc_final: 0.8219 (mmm) REVERT: C 357 ARG cc_start: 0.9052 (ptm-80) cc_final: 0.8467 (ptt180) REVERT: A 316 MET cc_start: 0.8327 (mmm) cc_final: 0.7994 (mmm) REVERT: A 333 SER cc_start: 0.9151 (m) cc_final: 0.8923 (m) REVERT: A 364 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8857 (t0) REVERT: B 125 MET cc_start: 0.9333 (ptp) cc_final: 0.8782 (pmm) REVERT: B 255 MET cc_start: 0.8424 (mtm) cc_final: 0.8190 (mtt) REVERT: B 568 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9097 (pp) REVERT: B 750 ASP cc_start: 0.8286 (t0) cc_final: 0.8054 (p0) outliers start: 32 outliers final: 15 residues processed: 112 average time/residue: 0.2558 time to fit residues: 47.7744 Evaluate side-chains 104 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 914 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 112 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 0.3980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.043822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.032832 restraints weight = 88193.768| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 4.07 r_work: 0.2514 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17115 Z= 0.248 Angle : 0.570 9.414 23329 Z= 0.288 Chirality : 0.044 0.342 2677 Planarity : 0.004 0.045 2946 Dihedral : 5.810 53.098 2759 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.82 % Allowed : 11.15 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.19), residues: 2022 helix: 1.91 (0.19), residues: 792 sheet: 0.22 (0.26), residues: 402 loop : -1.24 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 892 HIS 0.005 0.001 HIS B 394 PHE 0.029 0.001 PHE A 374 TYR 0.015 0.001 TYR B 509 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 2.024 Fit side-chains revert: symmetry clash REVERT: C 316 MET cc_start: 0.8803 (mmm) cc_final: 0.8256 (mmm) REVERT: C 357 ARG cc_start: 0.9069 (ptm-80) cc_final: 0.8458 (ptt180) REVERT: A 364 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8826 (t0) REVERT: B 568 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9126 (pp) REVERT: B 750 ASP cc_start: 0.8284 (t0) cc_final: 0.8042 (p0) outliers start: 33 outliers final: 22 residues processed: 111 average time/residue: 0.2518 time to fit residues: 46.5846 Evaluate side-chains 111 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 914 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 21 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 0.0770 chunk 125 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.044243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.033262 restraints weight = 87323.116| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 4.05 r_work: 0.2526 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17115 Z= 0.189 Angle : 0.596 24.378 23329 Z= 0.296 Chirality : 0.044 0.342 2677 Planarity : 0.004 0.045 2946 Dihedral : 5.689 52.683 2759 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.60 % Allowed : 11.81 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 2022 helix: 1.87 (0.19), residues: 802 sheet: 0.24 (0.26), residues: 414 loop : -1.32 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 892 HIS 0.005 0.001 HIS B 394 PHE 0.026 0.001 PHE A 374 TYR 0.013 0.001 TYR B 509 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.875 Fit side-chains revert: symmetry clash REVERT: C 316 MET cc_start: 0.8782 (mmm) cc_final: 0.8275 (mmm) REVERT: C 342 ARG cc_start: 0.8838 (ttp-110) cc_final: 0.8607 (ttp-110) REVERT: C 357 ARG cc_start: 0.9070 (ptm-80) cc_final: 0.8490 (ptt180) REVERT: A 316 MET cc_start: 0.8463 (mmm) cc_final: 0.8253 (mmm) REVERT: A 364 ASP cc_start: 0.9169 (t0) cc_final: 0.8836 (t0) REVERT: B 125 MET cc_start: 0.9338 (ptp) cc_final: 0.8794 (pmm) REVERT: B 568 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9097 (pp) REVERT: B 750 ASP cc_start: 0.8284 (t0) cc_final: 0.8060 (p0) outliers start: 29 outliers final: 23 residues processed: 109 average time/residue: 0.2753 time to fit residues: 48.1307 Evaluate side-chains 113 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 914 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 106 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 163 optimal weight: 0.5980 chunk 82 optimal weight: 0.0020 chunk 183 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 overall best weight: 2.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 378 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.043672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.032677 restraints weight = 88215.693| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 4.03 r_work: 0.2506 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17115 Z= 0.257 Angle : 0.617 23.131 23329 Z= 0.308 Chirality : 0.045 0.338 2677 Planarity : 0.004 0.044 2946 Dihedral : 5.749 53.330 2759 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.66 % Allowed : 11.98 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2022 helix: 1.83 (0.19), residues: 798 sheet: 0.22 (0.26), residues: 414 loop : -1.30 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 892 HIS 0.004 0.001 HIS B 394 PHE 0.035 0.001 PHE A 374 TYR 0.015 0.001 TYR B 509 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 2.078 Fit side-chains revert: symmetry clash REVERT: C 316 MET cc_start: 0.8785 (mmm) cc_final: 0.8274 (mmm) REVERT: C 342 ARG cc_start: 0.8847 (ttp-110) cc_final: 0.8624 (ttp-110) REVERT: C 357 ARG cc_start: 0.9071 (ptm-80) cc_final: 0.8548 (ptt180) REVERT: A 316 MET cc_start: 0.8388 (mmm) cc_final: 0.7962 (mmm) REVERT: A 341 PHE cc_start: 0.9043 (p90) cc_final: 0.8734 (p90) REVERT: A 364 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8836 (t0) REVERT: A 377 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8951 (m-10) REVERT: B 125 MET cc_start: 0.9345 (ptp) cc_final: 0.8784 (pmm) REVERT: B 568 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9124 (pp) outliers start: 30 outliers final: 23 residues processed: 107 average time/residue: 0.2674 time to fit residues: 46.3586 Evaluate side-chains 111 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 914 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 56 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 578 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.043120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.032093 restraints weight = 88497.413| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 4.04 r_work: 0.2484 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17115 Z= 0.322 Angle : 0.647 22.837 23329 Z= 0.324 Chirality : 0.046 0.363 2677 Planarity : 0.004 0.044 2946 Dihedral : 5.901 53.545 2759 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.77 % Allowed : 11.98 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 2022 helix: 1.75 (0.19), residues: 798 sheet: 0.35 (0.26), residues: 396 loop : -1.31 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 892 HIS 0.004 0.001 HIS B 394 PHE 0.025 0.001 PHE A 374 TYR 0.016 0.001 TYR B 509 ARG 0.007 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 2.126 Fit side-chains revert: symmetry clash REVERT: C 316 MET cc_start: 0.8733 (mmm) cc_final: 0.8229 (mmm) REVERT: C 357 ARG cc_start: 0.9070 (ptm-80) cc_final: 0.8531 (ptt180) REVERT: A 316 MET cc_start: 0.8392 (mmm) cc_final: 0.7879 (mmm) REVERT: A 364 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8853 (t0) REVERT: A 374 PHE cc_start: 0.8918 (p90) cc_final: 0.8572 (p90) REVERT: B 568 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9161 (pp) outliers start: 32 outliers final: 27 residues processed: 107 average time/residue: 0.2606 time to fit residues: 46.4701 Evaluate side-chains 112 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain D residue 718 ASP Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 914 THR Chi-restraints excluded: chain D residue 936 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 86 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.042997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.032027 restraints weight = 89437.450| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 4.03 r_work: 0.2472 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17115 Z= 0.349 Angle : 0.655 22.388 23329 Z= 0.329 Chirality : 0.046 0.351 2677 Planarity : 0.004 0.044 2946 Dihedral : 5.981 53.566 2759 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.60 % Allowed : 12.03 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 2022 helix: 1.69 (0.19), residues: 798 sheet: 0.19 (0.26), residues: 394 loop : -1.26 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 892 HIS 0.004 0.001 HIS B 394 PHE 0.020 0.001 PHE A 374 TYR 0.017 0.001 TYR B 509 ARG 0.007 0.000 ARG D 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 2.155 Fit side-chains revert: symmetry clash REVERT: C 316 MET cc_start: 0.8729 (mmm) cc_final: 0.8223 (mmm) REVERT: C 357 ARG cc_start: 0.9076 (ptm-80) cc_final: 0.8520 (ptt180) REVERT: A 316 MET cc_start: 0.8402 (mmm) cc_final: 0.7865 (mmm) REVERT: A 364 ASP cc_start: 0.9134 (t0) cc_final: 0.8843 (t0) REVERT: B 125 MET cc_start: 0.9317 (ptp) cc_final: 0.8768 (pmm) REVERT: B 568 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9175 (pp) outliers start: 29 outliers final: 26 residues processed: 104 average time/residue: 0.2668 time to fit residues: 46.2578 Evaluate side-chains 109 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 914 THR Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 914 THR Chi-restraints excluded: chain D residue 936 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 102 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 2 optimal weight: 0.0970 chunk 110 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN B 378 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.043714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.032605 restraints weight = 87907.518| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 4.09 r_work: 0.2505 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17115 Z= 0.209 Angle : 0.602 21.452 23329 Z= 0.299 Chirality : 0.044 0.333 2677 Planarity : 0.004 0.045 2946 Dihedral : 5.743 52.155 2759 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.55 % Allowed : 11.92 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.19), residues: 2022 helix: 1.81 (0.19), residues: 798 sheet: 0.36 (0.26), residues: 384 loop : -1.28 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 892 HIS 0.004 0.001 HIS B 394 PHE 0.017 0.001 PHE D 496 TYR 0.013 0.001 TYR B 509 ARG 0.007 0.000 ARG D 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7166.57 seconds wall clock time: 128 minutes 34.66 seconds (7714.66 seconds total)