Starting phenix.real_space_refine on Mon Feb 19 04:24:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ows_20216/02_2024/6ows_20216_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ows_20216/02_2024/6ows_20216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ows_20216/02_2024/6ows_20216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ows_20216/02_2024/6ows_20216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ows_20216/02_2024/6ows_20216_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ows_20216/02_2024/6ows_20216_updated.pdb" } resolution = 2.98 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= -0.000 sd= 1.000 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 P 6 5.49 5 S 135 5.16 5 C 15317 2.51 5 N 3825 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 771": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 813": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A ARG 963": "NH1" <-> "NH2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ASP 156": "OD1" <-> "OD2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 724": "NH1" <-> "NH2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ARG 809": "NH1" <-> "NH2" Residue "B ARG 813": "NH1" <-> "NH2" Residue "B ARG 833": "NH1" <-> "NH2" Residue "B ARG 910": "NH1" <-> "NH2" Residue "B ARG 961": "NH1" <-> "NH2" Residue "B ARG 963": "NH1" <-> "NH2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C ASP 429": "OD1" <-> "OD2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 724": "NH1" <-> "NH2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "C ARG 771": "NH1" <-> "NH2" Residue "C ARG 809": "NH1" <-> "NH2" Residue "C ARG 813": "NH1" <-> "NH2" Residue "C ARG 833": "NH1" <-> "NH2" Residue "C ARG 910": "NH1" <-> "NH2" Residue "C ARG 961": "NH1" <-> "NH2" Residue "C ARG 963": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23651 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7807 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 46, 'TRANS': 976} Chain: "B" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7807 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 46, 'TRANS': 976} Chain: "C" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7807 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 46, 'TRANS': 976} Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Time building chain proxies: 12.91, per 1000 atoms: 0.55 Number of scatterers: 23651 At special positions: 0 Unit cell: (116.6, 120.84, 142.04, 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) S 135 16.00 P 6 15.00 O 4368 8.00 N 3825 7.00 C 15317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.36 Conformation dependent library (CDL) restraints added in 4.7 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5718 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 21 sheets defined 48.7% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.12 Creating SS restraints... Processing helix chain 'A' and resid 3 through 5 No H-bonds generated for 'chain 'A' and resid 3 through 5' Processing helix chain 'A' and resid 9 through 24 removed outlier: 3.888A pdb=" N ILE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 60 removed outlier: 3.544A pdb=" N ASP A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 69 removed outlier: 3.635A pdb=" N ARG A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.579A pdb=" N LYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 162 through 165 No H-bonds generated for 'chain 'A' and resid 162 through 165' Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.714A pdb=" N VAL A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 194' Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.861A pdb=" N ASN A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.560A pdb=" N GLU A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 removed outlier: 3.604A pdb=" N VAL A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 358 " --> pdb=" O VAL A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 385 removed outlier: 4.064A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 4.210A pdb=" N VAL A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix removed outlier: 3.864A pdb=" N THR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 405 removed outlier: 4.450A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 422 removed outlier: 4.484A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 450 removed outlier: 3.647A pdb=" N SER A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.938A pdb=" N LEU A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 461 through 486 removed outlier: 3.787A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 509 through 531 removed outlier: 3.979A pdb=" N PHE A 513 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU A 525 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 555 removed outlier: 3.606A pdb=" N VAL A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A 541 " --> pdb=" O PRO A 537 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 542 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 Processing helix chain 'A' and resid 636 through 646 removed outlier: 4.069A pdb=" N SER A 641 " --> pdb=" O SER A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 684 through 697 removed outlier: 4.057A pdb=" N ASP A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.621A pdb=" N ASP A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 740 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 744 No H-bonds generated for 'chain 'A' and resid 742 through 744' Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 792 through 794 No H-bonds generated for 'chain 'A' and resid 792 through 794' Processing helix chain 'A' and resid 828 through 841 removed outlier: 3.893A pdb=" N GLU A 836 " --> pdb=" O MET A 832 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA A 840 " --> pdb=" O GLU A 836 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 861 Processing helix chain 'A' and resid 864 through 880 removed outlier: 3.508A pdb=" N MET A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A 875 " --> pdb=" O SER A 871 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 896 through 908 removed outlier: 4.177A pdb=" N GLY A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 905 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 945 removed outlier: 3.587A pdb=" N ALA A 930 " --> pdb=" O ILE A 926 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 959 removed outlier: 3.655A pdb=" N THR A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 955 " --> pdb=" O ILE A 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 956 " --> pdb=" O GLU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 973 Processing helix chain 'A' and resid 977 through 980 No H-bonds generated for 'chain 'A' and resid 977 through 980' Processing helix chain 'A' and resid 988 through 1010 removed outlier: 4.033A pdb=" N LEU A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1020 removed outlier: 3.791A pdb=" N ILE A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 9 through 24 removed outlier: 3.888A pdb=" N ILE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 60 removed outlier: 3.544A pdb=" N ASP B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.634A pdb=" N ARG B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.579A pdb=" N LYS B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 162 through 165 No H-bonds generated for 'chain 'B' and resid 162 through 165' Processing helix chain 'B' and resid 190 through 194 removed outlier: 3.713A pdb=" N VAL B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 190 through 194' Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 243 through 248 removed outlier: 3.861A pdb=" N ASN B 248 " --> pdb=" O GLU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 299 through 313 removed outlier: 3.560A pdb=" N GLU B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 359 removed outlier: 3.605A pdb=" N VAL B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 385 removed outlier: 4.063A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 4.209A pdb=" N VAL B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix removed outlier: 3.864A pdb=" N THR B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 405 removed outlier: 4.450A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 422 removed outlier: 4.484A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 450 removed outlier: 3.647A pdb=" N SER B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 439 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 4.041A pdb=" N LEU B 447 " --> pdb=" O ILE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 461 through 486 removed outlier: 3.787A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 Processing helix chain 'B' and resid 509 through 531 removed outlier: 3.979A pdb=" N PHE B 513 " --> pdb=" O PHE B 509 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B 525 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 531 " --> pdb=" O MET B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 555 removed outlier: 3.607A pdb=" N VAL B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE B 541 " --> pdb=" O PRO B 537 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 542 " --> pdb=" O MET B 538 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 549 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 592 Processing helix chain 'B' and resid 636 through 646 removed outlier: 4.068A pdb=" N SER B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 666 No H-bonds generated for 'chain 'B' and resid 664 through 666' Processing helix chain 'B' and resid 684 through 697 removed outlier: 4.058A pdb=" N ASP B 692 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU B 693 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.620A pdb=" N ASP B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 740 " --> pdb=" O ASP B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 744 No H-bonds generated for 'chain 'B' and resid 742 through 744' Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 777 through 779 No H-bonds generated for 'chain 'B' and resid 777 through 779' Processing helix chain 'B' and resid 792 through 794 No H-bonds generated for 'chain 'B' and resid 792 through 794' Processing helix chain 'B' and resid 828 through 841 removed outlier: 3.892A pdb=" N GLU B 836 " --> pdb=" O MET B 832 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA B 840 " --> pdb=" O GLU B 836 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 861 Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.508A pdb=" N MET B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL B 875 " --> pdb=" O SER B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 890 No H-bonds generated for 'chain 'B' and resid 888 through 890' Processing helix chain 'B' and resid 896 through 908 removed outlier: 4.176A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 905 " --> pdb=" O PHE B 901 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 945 removed outlier: 3.569A pdb=" N ALA B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 959 removed outlier: 3.656A pdb=" N THR B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 955 " --> pdb=" O ILE B 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 956 " --> pdb=" O GLU B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 973 Processing helix chain 'B' and resid 977 through 980 No H-bonds generated for 'chain 'B' and resid 977 through 980' Processing helix chain 'B' and resid 988 through 1010 removed outlier: 4.032A pdb=" N LEU B 993 " --> pdb=" O THR B 989 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 999 " --> pdb=" O THR B 995 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE B1010 " --> pdb=" O ILE B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1020 removed outlier: 3.792A pdb=" N ILE B1017 " --> pdb=" O PRO B1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B1020 " --> pdb=" O PHE B1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.888A pdb=" N ILE C 15 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 60 removed outlier: 3.544A pdb=" N ASP C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 69 removed outlier: 3.634A pdb=" N ARG C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 69 " --> pdb=" O ILE C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.579A pdb=" N LYS C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 162 through 165 No H-bonds generated for 'chain 'C' and resid 162 through 165' Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.715A pdb=" N VAL C 194 " --> pdb=" O PRO C 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 190 through 194' Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.861A pdb=" N ASN C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.560A pdb=" N GLU C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 359 removed outlier: 3.604A pdb=" N VAL C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 385 removed outlier: 4.064A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 4.210A pdb=" N VAL C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix removed outlier: 3.863A pdb=" N THR C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL C 382 " --> pdb=" O GLY C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 405 removed outlier: 4.449A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 422 removed outlier: 4.484A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 450 removed outlier: 3.646A pdb=" N SER C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 439 " --> pdb=" O MET C 435 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 4.041A pdb=" N LEU C 447 " --> pdb=" O ILE C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 461 through 486 removed outlier: 3.786A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE C 478 " --> pdb=" O MET C 474 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 509 through 531 removed outlier: 3.979A pdb=" N PHE C 513 " --> pdb=" O PHE C 509 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU C 525 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 531 " --> pdb=" O MET C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 555 removed outlier: 3.605A pdb=" N VAL C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE C 541 " --> pdb=" O PRO C 537 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 542 " --> pdb=" O MET C 538 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 544 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 549 " --> pdb=" O ILE C 545 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 554 " --> pdb=" O PHE C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 592 Processing helix chain 'C' and resid 636 through 646 removed outlier: 4.069A pdb=" N SER C 641 " --> pdb=" O SER C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 666 No H-bonds generated for 'chain 'C' and resid 664 through 666' Processing helix chain 'C' and resid 684 through 697 removed outlier: 4.056A pdb=" N ASP C 692 " --> pdb=" O LEU C 688 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 734 through 740 removed outlier: 3.621A pdb=" N ASP C 739 " --> pdb=" O SER C 735 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 740 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 744 No H-bonds generated for 'chain 'C' and resid 742 through 744' Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 777 through 779 No H-bonds generated for 'chain 'C' and resid 777 through 779' Processing helix chain 'C' and resid 792 through 794 No H-bonds generated for 'chain 'C' and resid 792 through 794' Processing helix chain 'C' and resid 828 through 841 removed outlier: 3.893A pdb=" N GLU C 836 " --> pdb=" O MET C 832 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA C 840 " --> pdb=" O GLU C 836 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS C 841 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 861 Processing helix chain 'C' and resid 864 through 880 removed outlier: 3.506A pdb=" N MET C 872 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 875 " --> pdb=" O SER C 871 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 880 " --> pdb=" O PHE C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 890 No H-bonds generated for 'chain 'C' and resid 888 through 890' Processing helix chain 'C' and resid 896 through 908 removed outlier: 4.175A pdb=" N GLY C 902 " --> pdb=" O LEU C 898 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 905 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 945 removed outlier: 3.588A pdb=" N ALA C 930 " --> pdb=" O ILE C 926 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 959 removed outlier: 3.656A pdb=" N THR C 954 " --> pdb=" O LEU C 950 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 955 " --> pdb=" O ILE C 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 956 " --> pdb=" O GLU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 973 Processing helix chain 'C' and resid 977 through 980 No H-bonds generated for 'chain 'C' and resid 977 through 980' Processing helix chain 'C' and resid 988 through 1010 removed outlier: 4.032A pdb=" N LEU C 993 " --> pdb=" O THR C 989 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 999 " --> pdb=" O THR C 995 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1020 removed outlier: 3.792A pdb=" N ILE C1017 " --> pdb=" O PRO C1013 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C1020 " --> pdb=" O PHE C1016 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= B, first strand: chain 'A' and resid 322 through 328 removed outlier: 7.215A pdb=" N LEU A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.479A pdb=" N MET A 759 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N MET A 184 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN A 761 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE A 186 " --> pdb=" O GLN A 761 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 763 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL A 188 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLN A 765 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL A 766 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER A 747 " --> pdb=" O VAL A 766 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 278 through 280 removed outlier: 6.702A pdb=" N THR A 625 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN A 604 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 623 " --> pdb=" O ASN A 604 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA A 606 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 621 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU A 608 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL A 619 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 620 " --> pdb=" O PHE A 573 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 672 through 677 removed outlier: 4.293A pdb=" N ILE A 821 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N MET A 706 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 715 through 722 removed outlier: 3.638A pdb=" N GLY A 715 " --> pdb=" O ALA A 803 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 801 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 781 through 783 Processing sheet with id= H, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= I, first strand: chain 'B' and resid 322 through 328 removed outlier: 7.215A pdb=" N LEU B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.480A pdb=" N MET B 759 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N MET B 184 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN B 761 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE B 186 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 763 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL B 188 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN B 765 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL B 766 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N SER B 747 " --> pdb=" O VAL B 766 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 278 through 280 removed outlier: 6.701A pdb=" N THR B 625 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN B 604 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE B 623 " --> pdb=" O ASN B 604 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA B 606 " --> pdb=" O VAL B 621 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 621 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU B 608 " --> pdb=" O VAL B 619 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL B 619 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 620 " --> pdb=" O PHE B 573 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 672 through 677 removed outlier: 4.291A pdb=" N ILE B 821 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 715 through 722 removed outlier: 3.639A pdb=" N GLY B 715 " --> pdb=" O ALA B 803 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 801 " --> pdb=" O ASN B 717 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 781 through 783 Processing sheet with id= O, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= P, first strand: chain 'C' and resid 322 through 328 removed outlier: 7.215A pdb=" N LEU C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.479A pdb=" N MET C 759 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N MET C 184 " --> pdb=" O MET C 759 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN C 761 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE C 186 " --> pdb=" O GLN C 761 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 763 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL C 188 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLN C 765 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL C 766 " --> pdb=" O SER C 747 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER C 747 " --> pdb=" O VAL C 766 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 278 through 280 removed outlier: 6.703A pdb=" N THR C 625 " --> pdb=" O LYS C 602 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN C 604 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE C 623 " --> pdb=" O ASN C 604 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA C 606 " --> pdb=" O VAL C 621 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C 621 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU C 608 " --> pdb=" O VAL C 619 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL C 619 " --> pdb=" O LEU C 608 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C 620 " --> pdb=" O PHE C 573 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 672 through 677 removed outlier: 4.292A pdb=" N ILE C 821 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 715 through 722 removed outlier: 3.638A pdb=" N GLY C 715 " --> pdb=" O ALA C 803 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 801 " --> pdb=" O ASN C 717 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 781 through 783 950 hydrogen bonds defined for protein. 2799 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: 8.86 Time building geometry restraints manager: 12.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3864 1.28 - 1.41: 5389 1.41 - 1.54: 14475 1.54 - 1.68: 83 1.68 - 1.81: 264 Bond restraints: 24075 Sorted by residual: bond pdb=" C LYS C 468 " pdb=" O LYS C 468 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.15e-02 7.56e+03 5.39e+01 bond pdb=" CA ASP B 578 " pdb=" C ASP B 578 " ideal model delta sigma weight residual 1.524 1.440 0.084 1.29e-02 6.01e+03 4.27e+01 bond pdb=" C ALA A 579 " pdb=" O ALA A 579 " ideal model delta sigma weight residual 1.236 1.157 0.079 1.21e-02 6.83e+03 4.21e+01 bond pdb=" C ASP B 578 " pdb=" O ASP B 578 " ideal model delta sigma weight residual 1.235 1.144 0.091 1.40e-02 5.10e+03 4.19e+01 bond pdb=" C ALA C 579 " pdb=" O ALA C 579 " ideal model delta sigma weight residual 1.235 1.167 0.068 1.22e-02 6.72e+03 3.13e+01 ... (remaining 24070 not shown) Histogram of bond angle deviations from ideal: 96.82 - 105.02: 569 105.02 - 113.22: 13455 113.22 - 121.42: 13213 121.42 - 129.61: 5248 129.61 - 137.81: 116 Bond angle restraints: 32601 Sorted by residual: angle pdb=" C LEU B 222 " pdb=" N PRO B 223 " pdb=" CA PRO B 223 " ideal model delta sigma weight residual 119.76 103.76 16.00 1.03e+00 9.43e-01 2.41e+02 angle pdb=" N PRO B 223 " pdb=" CA PRO B 223 " pdb=" C PRO B 223 " ideal model delta sigma weight residual 111.14 96.82 14.32 1.56e+00 4.11e-01 8.42e+01 angle pdb=" N ARG C 724 " pdb=" CA ARG C 724 " pdb=" C ARG C 724 " ideal model delta sigma weight residual 111.28 119.81 -8.53 1.09e+00 8.42e-01 6.12e+01 angle pdb=" N ARG B 724 " pdb=" CA ARG B 724 " pdb=" C ARG B 724 " ideal model delta sigma weight residual 111.28 118.83 -7.55 1.09e+00 8.42e-01 4.79e+01 angle pdb=" N ARG A 724 " pdb=" CA ARG A 724 " pdb=" C ARG A 724 " ideal model delta sigma weight residual 111.28 118.77 -7.49 1.09e+00 8.42e-01 4.72e+01 ... (remaining 32596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.86: 13659 24.86 - 49.72: 848 49.72 - 74.58: 107 74.58 - 99.43: 14 99.43 - 124.29: 3 Dihedral angle restraints: 14631 sinusoidal: 5790 harmonic: 8841 Sorted by residual: dihedral pdb=" CA ASP C 221 " pdb=" C ASP C 221 " pdb=" N LEU C 222 " pdb=" CA LEU C 222 " ideal model delta harmonic sigma weight residual -180.00 -150.01 -29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASP A 221 " pdb=" C ASP A 221 " pdb=" N LEU A 222 " pdb=" CA LEU A 222 " ideal model delta harmonic sigma weight residual -180.00 -150.10 -29.90 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ARG B 632 " pdb=" C ARG B 632 " pdb=" N THR B 633 " pdb=" CA THR B 633 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 14628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3732 0.121 - 0.242: 131 0.242 - 0.364: 8 0.364 - 0.485: 6 0.485 - 0.606: 2 Chirality restraints: 3879 Sorted by residual: chirality pdb=" CA TYR B 883 " pdb=" N TYR B 883 " pdb=" C TYR B 883 " pdb=" CB TYR B 883 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.19e+00 chirality pdb=" CA TYR C 883 " pdb=" N TYR C 883 " pdb=" C TYR C 883 " pdb=" CB TYR C 883 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CA ARG C 724 " pdb=" N ARG C 724 " pdb=" C ARG C 724 " pdb=" CB ARG C 724 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 ... (remaining 3876 not shown) Planarity restraints: 4086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 883 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C TYR B 883 " -0.067 2.00e-02 2.50e+03 pdb=" O TYR B 883 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU B 884 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 576 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C PRO B 576 " 0.062 2.00e-02 2.50e+03 pdb=" O PRO B 576 " -0.022 2.00e-02 2.50e+03 pdb=" N SER B 577 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 575 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.17e+01 pdb=" C LEU C 575 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU C 575 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO C 576 " 0.020 2.00e-02 2.50e+03 ... (remaining 4083 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4099 2.75 - 3.29: 21053 3.29 - 3.83: 36771 3.83 - 4.36: 45047 4.36 - 4.90: 77267 Nonbonded interactions: 184237 Sorted by model distance: nonbonded pdb=" NZ LYS C 468 " pdb=" O13 PTY C1102 " model vdw 2.216 2.520 nonbonded pdb=" O THR C 471 " pdb=" OG SER C 475 " model vdw 2.230 2.440 nonbonded pdb=" O THR A 471 " pdb=" OG SER A 475 " model vdw 2.230 2.440 nonbonded pdb=" O THR B 471 " pdb=" OG SER B 475 " model vdw 2.231 2.440 nonbonded pdb=" OD1 ASP C 723 " pdb=" OE1 GLU C 725 " model vdw 2.233 3.040 ... (remaining 184232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 1023 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C18 or name C2 \ or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or na \ me O4 or name O7 or name P1 )) or (resid 1102 and (name C1 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C5 \ or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 \ or name O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'B' and (resid 1 through 1023 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C18 or name C2 \ or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or na \ me O4 or name O7 or name P1 )) or resid 1102)) selection = (chain 'C' and (resid 1 through 1023 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C18 or name C2 \ or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name \ N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or na \ me O4 or name O7 or name P1 )) or (resid 1102 and (name C1 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C5 \ or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 \ or name O14 or name O30 or name O4 or name O7 or name P1 )))) } 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: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 22.500 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 68.680 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.009 0.115 24075 Z= 0.587 Angle : 1.042 17.700 32601 Z= 0.562 Chirality : 0.061 0.606 3879 Planarity : 0.008 0.081 4086 Dihedral : 15.742 124.293 8913 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.69 % Favored : 96.15 % Rotamer: Outliers : 6.03 % Allowed : 6.81 % Favored : 87.16 % Cbeta Deviations : 0.10 % 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: -5.39 (0.11), residues: 3063 helix: -4.36 (0.06), residues: 1530 sheet: -2.77 (0.19), residues: 498 loop : -2.16 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 800 HIS 0.004 0.001 HIS A 503 PHE 0.022 0.002 PHE A 569 TYR 0.039 0.002 TYR C 883 ARG 0.005 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 521 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLN cc_start: 0.8991 (mt0) cc_final: 0.8682 (mt0) REVERT: A 79 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8763 (t) REVERT: A 89 GLU cc_start: 0.7775 (tt0) cc_final: 0.7457 (tp30) REVERT: A 102 MET cc_start: 0.8364 (mmm) cc_final: 0.8156 (mmt) REVERT: A 128 GLN cc_start: 0.7764 (mp10) cc_final: 0.7402 (mp10) REVERT: A 130 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6393 (pp20) REVERT: A 132 SER cc_start: 0.7857 (t) cc_final: 0.7644 (m) REVERT: A 164 GLU cc_start: 0.8004 (tp30) cc_final: 0.7787 (mm-30) REVERT: A 357 LEU cc_start: 0.8114 (mm) cc_final: 0.7648 (tp) REVERT: A 404 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7855 (pt) REVERT: A 517 PHE cc_start: 0.6539 (t80) cc_final: 0.6335 (t80) REVERT: A 525 GLU cc_start: 0.8198 (tt0) cc_final: 0.7818 (tp30) REVERT: A 529 LEU cc_start: 0.8832 (tp) cc_final: 0.8629 (mm) REVERT: A 637 SER cc_start: 0.8323 (t) cc_final: 0.8002 (m) REVERT: A 783 MET cc_start: 0.9017 (tpt) cc_final: 0.8717 (tpp) REVERT: A 844 LYS cc_start: 0.8584 (tttm) cc_final: 0.8108 (mppt) REVERT: A 861 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7548 (mp0) REVERT: A 864 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6864 (tpp) REVERT: A 949 SER cc_start: 0.7196 (OUTLIER) cc_final: 0.6994 (p) REVERT: B 1 MET cc_start: 0.4830 (mmm) cc_final: 0.3912 (mpp) REVERT: B 128 GLN cc_start: 0.7939 (mp10) cc_final: 0.7473 (mp10) REVERT: B 138 MET cc_start: 0.8882 (ptm) cc_final: 0.8647 (ptm) REVERT: B 357 LEU cc_start: 0.8178 (mm) cc_final: 0.7666 (tp) REVERT: B 379 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8149 (t) REVERT: B 404 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8054 (pt) REVERT: B 420 MET cc_start: 0.8746 (mtm) cc_final: 0.7950 (mtp) REVERT: B 637 SER cc_start: 0.8400 (t) cc_final: 0.8104 (m) REVERT: B 656 MET cc_start: 0.8249 (mmm) cc_final: 0.7825 (tpp) REVERT: B 706 MET cc_start: 0.5807 (ttt) cc_final: 0.5502 (mtp) REVERT: B 745 MET cc_start: 0.8220 (mtm) cc_final: 0.7792 (mtm) REVERT: B 770 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8685 (m) REVERT: B 844 LYS cc_start: 0.8800 (tttm) cc_final: 0.8152 (mppt) REVERT: B 861 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7471 (mp0) REVERT: B 872 MET cc_start: 0.8201 (mtp) cc_final: 0.7986 (mtm) REVERT: B 904 ILE cc_start: 0.7908 (pt) cc_final: 0.7631 (pp) REVERT: B 967 MET cc_start: 0.8833 (mtp) cc_final: 0.8585 (mtp) REVERT: C 67 ARG cc_start: 0.8230 (ttp80) cc_final: 0.8022 (ttm-80) REVERT: C 128 GLN cc_start: 0.7814 (mp10) cc_final: 0.7537 (mp10) REVERT: C 130 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6431 (pp20) REVERT: C 184 MET cc_start: 0.9157 (tpp) cc_final: 0.8938 (tpp) REVERT: C 292 GLN cc_start: 0.8800 (mt0) cc_final: 0.8452 (mt0) REVERT: C 321 MET cc_start: 0.8729 (mtt) cc_final: 0.8496 (mtt) REVERT: C 379 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8061 (t) REVERT: C 404 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7969 (pt) REVERT: C 420 MET cc_start: 0.8687 (mtm) cc_final: 0.8278 (mtm) REVERT: C 454 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8576 (mm) REVERT: C 458 PHE cc_start: 0.8684 (m-80) cc_final: 0.8479 (m-80) REVERT: C 529 LEU cc_start: 0.8969 (tp) cc_final: 0.8573 (mm) REVERT: C 637 SER cc_start: 0.8419 (t) cc_final: 0.8098 (m) REVERT: C 639 MET cc_start: 0.8075 (ttm) cc_final: 0.7780 (mtm) REVERT: C 656 MET cc_start: 0.8182 (mmm) cc_final: 0.7456 (tpp) REVERT: C 783 MET cc_start: 0.9096 (tpt) cc_final: 0.8855 (tpp) REVERT: C 813 ARG cc_start: 0.8402 (mmt90) cc_final: 0.8191 (mpt-90) REVERT: C 844 LYS cc_start: 0.8699 (tttm) cc_final: 0.8210 (mmmt) REVERT: C 861 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7607 (mp0) REVERT: C 864 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6809 (tpp) REVERT: C 915 ASP cc_start: 0.8073 (p0) cc_final: 0.7856 (p0) REVERT: C 942 MET cc_start: 0.7906 (ttm) cc_final: 0.7703 (tmt) outliers start: 155 outliers final: 31 residues processed: 639 average time/residue: 1.3086 time to fit residues: 962.3174 Evaluate side-chains 347 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 305 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 738 SER Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 664 ASP Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 738 SER Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 128 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 277 optimal weight: 0.7980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 237 GLN A 248 ASN A 574 GLN A 586 ASN A 593 ASN A 617 GLN A 644 ASN A 717 ASN A 779 ASN A 788 GLN A 805 GLN B 44 ASN B 120 GLN B 205 ASN B 237 GLN B 248 ASN B 586 ASN B 593 ASN B 617 GLN B 644 ASN B 717 ASN B 779 ASN B 805 GLN C 44 ASN C 74 ASN C 120 GLN C 205 ASN C 237 GLN C 248 ASN C 574 GLN C 586 ASN C 593 ASN C 617 GLN C 644 ASN C 717 ASN C 779 ASN C 805 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24075 Z= 0.218 Angle : 0.634 10.984 32601 Z= 0.322 Chirality : 0.042 0.162 3879 Planarity : 0.005 0.072 4086 Dihedral : 9.351 105.292 3451 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.46 % Allowed : 16.34 % Favored : 80.20 % 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: -3.56 (0.13), residues: 3063 helix: -2.51 (0.10), residues: 1617 sheet: -1.96 (0.20), residues: 501 loop : -1.77 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.003 0.001 HIS A 360 PHE 0.023 0.002 PHE B 824 TYR 0.012 0.001 TYR C 883 ARG 0.006 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 328 time to evaluate : 2.809 Fit side-chains revert: symmetry clash REVERT: A 42 GLN cc_start: 0.9076 (mt0) cc_final: 0.8621 (mt0) REVERT: A 89 GLU cc_start: 0.7635 (tt0) cc_final: 0.7283 (tp30) REVERT: A 128 GLN cc_start: 0.7403 (mp10) cc_final: 0.7077 (mp10) REVERT: A 164 GLU cc_start: 0.8019 (tp30) cc_final: 0.7760 (mm-30) REVERT: A 259 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8772 (m) REVERT: A 425 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5724 (tp) REVERT: A 525 GLU cc_start: 0.8151 (tt0) cc_final: 0.7783 (tp30) REVERT: A 529 LEU cc_start: 0.8692 (tp) cc_final: 0.8411 (mm) REVERT: A 590 GLN cc_start: 0.7706 (tp40) cc_final: 0.7324 (mt0) REVERT: A 637 SER cc_start: 0.8346 (t) cc_final: 0.8002 (m) REVERT: A 649 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.7841 (p0) REVERT: A 656 MET cc_start: 0.8148 (tpt) cc_final: 0.7809 (tpt) REVERT: A 783 MET cc_start: 0.9015 (tpt) cc_final: 0.8703 (tpp) REVERT: A 844 LYS cc_start: 0.8585 (tttm) cc_final: 0.8117 (mppt) REVERT: A 849 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7944 (mt-10) REVERT: A 864 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.6871 (tpp) REVERT: A 893 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8124 (mmp) REVERT: A 963 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7595 (ttt180) REVERT: B 1 MET cc_start: 0.5071 (mmm) cc_final: 0.4173 (mpp) REVERT: B 67 ARG cc_start: 0.8216 (ptm-80) cc_final: 0.7745 (ptm-80) REVERT: B 128 GLN cc_start: 0.7426 (mp10) cc_final: 0.6995 (mp10) REVERT: B 138 MET cc_start: 0.8685 (ptm) cc_final: 0.8454 (ptm) REVERT: B 164 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7864 (pm20) REVERT: B 259 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8862 (m) REVERT: B 292 GLN cc_start: 0.8268 (mt0) cc_final: 0.7945 (mt0) REVERT: B 525 GLU cc_start: 0.8250 (tt0) cc_final: 0.8013 (tp30) REVERT: B 529 LEU cc_start: 0.8632 (mt) cc_final: 0.8414 (mm) REVERT: B 538 MET cc_start: 0.6706 (mmm) cc_final: 0.6492 (mtp) REVERT: B 553 MET cc_start: 0.8334 (mtp) cc_final: 0.7795 (mmp) REVERT: B 590 GLN cc_start: 0.7765 (tp40) cc_final: 0.7494 (mt0) REVERT: B 637 SER cc_start: 0.8466 (t) cc_final: 0.8137 (m) REVERT: B 706 MET cc_start: 0.6011 (ttt) cc_final: 0.5756 (mtp) REVERT: B 745 MET cc_start: 0.8236 (mtm) cc_final: 0.7965 (mtm) REVERT: B 824 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6493 (p90) REVERT: B 844 LYS cc_start: 0.8758 (tttm) cc_final: 0.8291 (mmpt) REVERT: B 952 GLU cc_start: 0.8311 (mp0) cc_final: 0.7967 (mp0) REVERT: B 963 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7337 (ttm-80) REVERT: C 7 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7363 (ptt90) REVERT: C 112 LYS cc_start: 0.8380 (mtmm) cc_final: 0.7903 (ptpt) REVERT: C 292 GLN cc_start: 0.8443 (mt0) cc_final: 0.8111 (mt0) REVERT: C 321 MET cc_start: 0.8842 (mtt) cc_final: 0.8523 (mtt) REVERT: C 355 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7762 (mtp) REVERT: C 420 MET cc_start: 0.8305 (mtm) cc_final: 0.8010 (mtp) REVERT: C 449 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8017 (mp) REVERT: C 454 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8498 (mm) REVERT: C 538 MET cc_start: 0.6747 (mmm) cc_final: 0.6214 (ttp) REVERT: C 783 MET cc_start: 0.9050 (tpt) cc_final: 0.8823 (tpp) REVERT: C 824 PHE cc_start: 0.6832 (t80) cc_final: 0.6622 (t80) REVERT: C 844 LYS cc_start: 0.8686 (tttm) cc_final: 0.8226 (mmmt) REVERT: C 864 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.6884 (tpp) REVERT: C 942 MET cc_start: 0.7754 (ttm) cc_final: 0.7540 (tmt) REVERT: C 952 GLU cc_start: 0.8315 (mp0) cc_final: 0.8059 (mp0) outliers start: 89 outliers final: 21 residues processed: 384 average time/residue: 1.5011 time to fit residues: 656.2135 Evaluate side-chains 307 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 272 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 864 MET Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 963 ARG Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 824 PHE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 963 ARG Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 247 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 223 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN B 120 GLN B 292 GLN B 788 GLN C 120 GLN C 788 GLN C 863 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24075 Z= 0.248 Angle : 0.605 10.424 32601 Z= 0.303 Chirality : 0.042 0.160 3879 Planarity : 0.004 0.056 4086 Dihedral : 7.875 83.914 3405 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.97 % Allowed : 17.62 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.22 (0.14), residues: 3063 helix: -1.28 (0.12), residues: 1605 sheet: -1.34 (0.21), residues: 510 loop : -1.48 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 187 HIS 0.005 0.001 HIS A 360 PHE 0.022 0.001 PHE A 4 TYR 0.011 0.001 TYR B 883 ARG 0.006 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 286 time to evaluate : 2.566 Fit side-chains REVERT: A 42 GLN cc_start: 0.9018 (mt0) cc_final: 0.8568 (mt0) REVERT: A 68 GLU cc_start: 0.7572 (mp0) cc_final: 0.7354 (mp0) REVERT: A 89 GLU cc_start: 0.7600 (tt0) cc_final: 0.7260 (tp30) REVERT: A 111 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8283 (pp) REVERT: A 120 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8312 (mm110) REVERT: A 128 GLN cc_start: 0.7343 (mp10) cc_final: 0.6972 (mp10) REVERT: A 259 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8819 (m) REVERT: A 425 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5745 (tp) REVERT: A 525 GLU cc_start: 0.8146 (tt0) cc_final: 0.7942 (mm-30) REVERT: A 529 LEU cc_start: 0.8647 (tp) cc_final: 0.8267 (mm) REVERT: A 539 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7459 (mmt) REVERT: A 590 GLN cc_start: 0.7657 (tp40) cc_final: 0.6979 (tp-100) REVERT: A 649 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.7805 (p0) REVERT: A 656 MET cc_start: 0.8313 (tpt) cc_final: 0.8107 (tpt) REVERT: A 695 MET cc_start: 0.8519 (tpp) cc_final: 0.8037 (mmt) REVERT: A 783 MET cc_start: 0.9019 (tpt) cc_final: 0.8731 (tpp) REVERT: A 844 LYS cc_start: 0.8574 (tttm) cc_final: 0.8163 (mppt) REVERT: A 893 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7491 (mpm) REVERT: A 952 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: A 963 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7674 (ttt180) REVERT: A 970 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7585 (mt) REVERT: B 1 MET cc_start: 0.5387 (mmm) cc_final: 0.4455 (mpp) REVERT: B 111 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8280 (pp) REVERT: B 128 GLN cc_start: 0.7428 (mp10) cc_final: 0.7097 (mp10) REVERT: B 138 MET cc_start: 0.8743 (ptm) cc_final: 0.8532 (ptm) REVERT: B 221 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: B 259 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8770 (m) REVERT: B 292 GLN cc_start: 0.8182 (mt0) cc_final: 0.7970 (mt0) REVERT: B 395 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7461 (mmp) REVERT: B 425 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5422 (tp) REVERT: B 553 MET cc_start: 0.8259 (mtp) cc_final: 0.7815 (mmp) REVERT: B 590 GLN cc_start: 0.7798 (tp40) cc_final: 0.7418 (tm-30) REVERT: B 706 MET cc_start: 0.6214 (ttt) cc_final: 0.5930 (mtp) REVERT: B 824 PHE cc_start: 0.6837 (t80) cc_final: 0.6561 (p90) REVERT: B 844 LYS cc_start: 0.8790 (tttm) cc_final: 0.8380 (mmpt) REVERT: B 861 GLU cc_start: 0.8365 (tp30) cc_final: 0.8160 (mm-30) REVERT: B 868 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7527 (mp) REVERT: B 963 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7610 (ttt180) REVERT: C 73 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8724 (ptpp) REVERT: C 134 SER cc_start: 0.8264 (m) cc_final: 0.8024 (p) REVERT: C 164 GLU cc_start: 0.7521 (pm20) cc_final: 0.7059 (pm20) REVERT: C 292 GLN cc_start: 0.8432 (mt0) cc_final: 0.8126 (mt0) REVERT: C 420 MET cc_start: 0.8517 (mtm) cc_final: 0.8254 (mtp) REVERT: C 425 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5646 (tp) REVERT: C 449 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8155 (tt) REVERT: C 512 TRP cc_start: 0.7517 (t60) cc_final: 0.7253 (t60) REVERT: C 538 MET cc_start: 0.6902 (mmm) cc_final: 0.6397 (mtp) REVERT: C 656 MET cc_start: 0.7085 (mmt) cc_final: 0.6696 (tpt) REVERT: C 783 MET cc_start: 0.9032 (tpt) cc_final: 0.8823 (tpp) REVERT: C 824 PHE cc_start: 0.6924 (t80) cc_final: 0.6648 (t80) REVERT: C 835 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8331 (mmm) REVERT: C 844 LYS cc_start: 0.8695 (tttm) cc_final: 0.8188 (mmmt) REVERT: C 864 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.6939 (tpp) REVERT: C 893 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8204 (mmp) REVERT: C 904 ILE cc_start: 0.7519 (pt) cc_final: 0.7290 (pp) REVERT: C 942 MET cc_start: 0.7711 (ttm) cc_final: 0.7486 (tmt) REVERT: C 952 GLU cc_start: 0.8242 (mp0) cc_final: 0.7875 (mp0) REVERT: C 970 LEU cc_start: 0.7888 (pp) cc_final: 0.7674 (mt) outliers start: 102 outliers final: 24 residues processed: 358 average time/residue: 1.3829 time to fit residues: 567.7863 Evaluate side-chains 309 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 263 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 952 GLU Chi-restraints excluded: chain A residue 963 ARG Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 963 ARG Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 893 MET Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 997 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 144 optimal weight: 0.0670 chunk 30 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 295 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 604 ASN C 120 GLN C 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24075 Z= 0.188 Angle : 0.558 10.524 32601 Z= 0.278 Chirality : 0.041 0.211 3879 Planarity : 0.004 0.051 4086 Dihedral : 7.108 60.056 3398 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.85 % Allowed : 17.70 % Favored : 78.45 % 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: -1.42 (0.15), residues: 3063 helix: -0.53 (0.13), residues: 1578 sheet: -0.93 (0.21), residues: 510 loop : -1.34 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 512 HIS 0.004 0.001 HIS A 360 PHE 0.019 0.001 PHE B 824 TYR 0.012 0.001 TYR C 883 ARG 0.006 0.000 ARG C 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 285 time to evaluate : 2.784 Fit side-chains REVERT: A 42 GLN cc_start: 0.9098 (mt0) cc_final: 0.8547 (mt0) REVERT: A 68 GLU cc_start: 0.7737 (mp0) cc_final: 0.7444 (mp0) REVERT: A 89 GLU cc_start: 0.7592 (tt0) cc_final: 0.7273 (tp30) REVERT: A 120 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8283 (mm110) REVERT: A 128 GLN cc_start: 0.7251 (mp10) cc_final: 0.6888 (mp10) REVERT: A 259 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8853 (m) REVERT: A 425 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5611 (tp) REVERT: A 525 GLU cc_start: 0.8169 (tt0) cc_final: 0.7917 (mm-30) REVERT: A 529 LEU cc_start: 0.8698 (tp) cc_final: 0.8231 (mm) REVERT: A 539 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7468 (mmt) REVERT: A 590 GLN cc_start: 0.7644 (tp40) cc_final: 0.7009 (tp-100) REVERT: A 637 SER cc_start: 0.8325 (t) cc_final: 0.7900 (m) REVERT: A 649 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7722 (p0) REVERT: A 783 MET cc_start: 0.9020 (tpt) cc_final: 0.8758 (tpp) REVERT: A 844 LYS cc_start: 0.8657 (tttm) cc_final: 0.8347 (mmpt) REVERT: A 849 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 888 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7274 (tt) REVERT: A 963 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7717 (ttt180) REVERT: B 1 MET cc_start: 0.5495 (mmm) cc_final: 0.4550 (mpp) REVERT: B 128 GLN cc_start: 0.7373 (mp10) cc_final: 0.7079 (mp10) REVERT: B 221 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: B 259 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8792 (m) REVERT: B 292 GLN cc_start: 0.8127 (mt0) cc_final: 0.7873 (mt0) REVERT: B 395 MET cc_start: 0.7623 (mtp) cc_final: 0.7373 (mmp) REVERT: B 425 LEU cc_start: 0.5855 (OUTLIER) cc_final: 0.5274 (tp) REVERT: B 529 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8075 (mm) REVERT: B 553 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7700 (mmm) REVERT: B 590 GLN cc_start: 0.7817 (tp40) cc_final: 0.7240 (tp-100) REVERT: B 630 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8751 (ptpp) REVERT: B 637 SER cc_start: 0.8291 (t) cc_final: 0.7902 (m) REVERT: B 706 MET cc_start: 0.6061 (ttt) cc_final: 0.5809 (mtp) REVERT: B 824 PHE cc_start: 0.6776 (t80) cc_final: 0.6532 (p90) REVERT: B 844 LYS cc_start: 0.8723 (tttm) cc_final: 0.8358 (mmpt) REVERT: B 864 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6264 (tpp) REVERT: B 868 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7287 (mp) REVERT: B 963 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7778 (ttt180) REVERT: C 164 GLU cc_start: 0.7702 (pm20) cc_final: 0.7083 (pm20) REVERT: C 229 LEU cc_start: 0.7927 (mt) cc_final: 0.7639 (mp) REVERT: C 292 GLN cc_start: 0.8396 (mt0) cc_final: 0.8076 (mt0) REVERT: C 420 MET cc_start: 0.8401 (mtm) cc_final: 0.8174 (mtp) REVERT: C 425 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5651 (tp) REVERT: C 449 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8220 (tt) REVERT: C 538 MET cc_start: 0.6893 (mmm) cc_final: 0.6396 (mtp) REVERT: C 539 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7348 (mmt) REVERT: C 783 MET cc_start: 0.9037 (tpt) cc_final: 0.8832 (tpp) REVERT: C 824 PHE cc_start: 0.6841 (t80) cc_final: 0.6548 (t80) REVERT: C 835 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8304 (mmm) REVERT: C 844 LYS cc_start: 0.8675 (tttm) cc_final: 0.8180 (mmmt) REVERT: C 864 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.6923 (tpp) REVERT: C 893 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8091 (mmp) REVERT: C 952 GLU cc_start: 0.8327 (mp0) cc_final: 0.7991 (mp0) REVERT: C 997 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7735 (m) outliers start: 99 outliers final: 28 residues processed: 352 average time/residue: 1.3880 time to fit residues: 558.8649 Evaluate side-chains 312 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 262 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 963 ARG Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 864 MET Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 963 ARG Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 893 MET Chi-restraints excluded: chain C residue 997 VAL Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 252 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 ASN A 805 GLN B 108 GLN B 120 GLN B 701 ASN B 859 GLN C 120 GLN C 701 ASN C 717 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24075 Z= 0.355 Angle : 0.642 11.266 32601 Z= 0.319 Chirality : 0.045 0.192 3879 Planarity : 0.004 0.045 4086 Dihedral : 7.208 61.026 3397 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 4.55 % Allowed : 18.24 % Favored : 77.21 % 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: -1.27 (0.15), residues: 3063 helix: -0.37 (0.13), residues: 1587 sheet: -0.87 (0.22), residues: 510 loop : -1.35 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 610 HIS 0.007 0.001 HIS A 360 PHE 0.019 0.002 PHE C 672 TYR 0.018 0.002 TYR C 883 ARG 0.007 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 258 time to evaluate : 2.819 Fit side-chains REVERT: A 1 MET cc_start: 0.6351 (mmm) cc_final: 0.5855 (mpp) REVERT: A 68 GLU cc_start: 0.7758 (mp0) cc_final: 0.7424 (mp0) REVERT: A 89 GLU cc_start: 0.7652 (tt0) cc_final: 0.7309 (tp30) REVERT: A 101 GLU cc_start: 0.8166 (tp30) cc_final: 0.7963 (tp30) REVERT: A 128 GLN cc_start: 0.7422 (mp10) cc_final: 0.7077 (mp10) REVERT: A 529 LEU cc_start: 0.8731 (tp) cc_final: 0.8411 (mm) REVERT: A 539 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7435 (mmt) REVERT: A 590 GLN cc_start: 0.7656 (tp40) cc_final: 0.7073 (tp-100) REVERT: A 649 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7765 (p0) REVERT: A 706 MET cc_start: 0.7000 (mtp) cc_final: 0.6052 (tpp) REVERT: A 783 MET cc_start: 0.9006 (tpt) cc_final: 0.8726 (tpp) REVERT: A 824 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6515 (p90) REVERT: A 844 LYS cc_start: 0.8607 (tttm) cc_final: 0.8102 (mppt) REVERT: A 888 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7223 (tt) REVERT: A 963 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7634 (ttt180) REVERT: B 1 MET cc_start: 0.5809 (mmm) cc_final: 0.4889 (mpp) REVERT: B 4 PHE cc_start: 0.8263 (t80) cc_final: 0.7845 (t80) REVERT: B 67 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8173 (ptm160) REVERT: B 108 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8451 (mm-40) REVERT: B 128 GLN cc_start: 0.7427 (mp10) cc_final: 0.7115 (mp10) REVERT: B 221 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: B 529 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8011 (mm) REVERT: B 538 MET cc_start: 0.7143 (mmm) cc_final: 0.6757 (mtp) REVERT: B 553 MET cc_start: 0.8270 (mtp) cc_final: 0.7815 (mmp) REVERT: B 706 MET cc_start: 0.6547 (ttt) cc_final: 0.6112 (mtp) REVERT: B 844 LYS cc_start: 0.8682 (tttm) cc_final: 0.8323 (mmpt) REVERT: B 907 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6645 (mm) REVERT: B 963 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7744 (ttt180) REVERT: C 164 GLU cc_start: 0.7817 (pm20) cc_final: 0.7110 (pm20) REVERT: C 256 ASN cc_start: 0.8028 (p0) cc_final: 0.7815 (p0) REVERT: C 292 GLN cc_start: 0.8393 (mt0) cc_final: 0.8123 (mt0) REVERT: C 353 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7812 (mp) REVERT: C 425 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.5749 (tp) REVERT: C 449 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8296 (tt) REVERT: C 538 MET cc_start: 0.7103 (mmm) cc_final: 0.6551 (mtp) REVERT: C 639 MET cc_start: 0.7708 (mtm) cc_final: 0.7508 (mtm) REVERT: C 824 PHE cc_start: 0.7111 (t80) cc_final: 0.6851 (t80) REVERT: C 835 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8317 (mmm) REVERT: C 844 LYS cc_start: 0.8717 (tttm) cc_final: 0.8186 (mmmt) REVERT: C 861 GLU cc_start: 0.8222 (tp30) cc_final: 0.7955 (tt0) REVERT: C 864 MET cc_start: 0.7909 (ttm) cc_final: 0.6896 (tpp) REVERT: C 893 MET cc_start: 0.8458 (mmp) cc_final: 0.8225 (mmp) REVERT: C 907 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6582 (mm) outliers start: 117 outliers final: 48 residues processed: 348 average time/residue: 1.4253 time to fit residues: 571.7395 Evaluate side-chains 309 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 245 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 824 PHE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 963 ARG Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 963 ARG Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 835 MET Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 997 VAL Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.9990 chunk 266 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 173 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 296 optimal weight: 0.9980 chunk 245 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 155 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 691 GLN B 108 GLN B 120 GLN B 691 GLN C 120 GLN C 691 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24075 Z= 0.189 Angle : 0.570 11.400 32601 Z= 0.281 Chirality : 0.041 0.202 3879 Planarity : 0.004 0.044 4086 Dihedral : 6.735 55.939 3394 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.58 % Allowed : 19.41 % Favored : 77.01 % 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: -0.80 (0.15), residues: 3063 helix: -0.01 (0.13), residues: 1590 sheet: -0.74 (0.21), residues: 543 loop : -1.04 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 886 HIS 0.005 0.001 HIS C 360 PHE 0.024 0.001 PHE B 824 TYR 0.014 0.001 TYR C 883 ARG 0.007 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 254 time to evaluate : 2.893 Fit side-chains REVERT: A 1 MET cc_start: 0.6428 (mmm) cc_final: 0.5899 (mpp) REVERT: A 68 GLU cc_start: 0.7736 (mp0) cc_final: 0.7444 (mp0) REVERT: A 89 GLU cc_start: 0.7639 (tt0) cc_final: 0.7312 (tp30) REVERT: A 120 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8387 (mm110) REVERT: A 128 GLN cc_start: 0.7422 (mp10) cc_final: 0.7087 (mp10) REVERT: A 134 SER cc_start: 0.8510 (m) cc_final: 0.8228 (t) REVERT: A 529 LEU cc_start: 0.8700 (tp) cc_final: 0.8288 (mm) REVERT: A 539 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7478 (mmp) REVERT: A 590 GLN cc_start: 0.7653 (tp40) cc_final: 0.7121 (tp-100) REVERT: A 649 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7555 (p0) REVERT: A 695 MET cc_start: 0.8391 (tpp) cc_final: 0.7867 (mmt) REVERT: A 706 MET cc_start: 0.6524 (mtp) cc_final: 0.5407 (tpt) REVERT: A 783 MET cc_start: 0.9045 (tpt) cc_final: 0.8768 (tpp) REVERT: A 824 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6477 (p90) REVERT: A 844 LYS cc_start: 0.8579 (tttm) cc_final: 0.8098 (mppt) REVERT: A 888 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7205 (tt) REVERT: A 963 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7724 (ttt180) REVERT: B 1 MET cc_start: 0.5787 (mmm) cc_final: 0.4887 (mpp) REVERT: B 4 PHE cc_start: 0.8295 (t80) cc_final: 0.7893 (t80) REVERT: B 108 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8404 (mm-40) REVERT: B 128 GLN cc_start: 0.7281 (mp10) cc_final: 0.7029 (mp10) REVERT: B 221 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: B 538 MET cc_start: 0.7119 (mmm) cc_final: 0.6695 (mtp) REVERT: B 553 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7635 (mmm) REVERT: B 632 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6737 (ttm170) REVERT: B 706 MET cc_start: 0.6287 (ttt) cc_final: 0.5983 (mtp) REVERT: B 844 LYS cc_start: 0.8641 (tttm) cc_final: 0.8319 (mmpt) REVERT: B 963 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7805 (ttt180) REVERT: C 164 GLU cc_start: 0.7841 (pm20) cc_final: 0.7218 (pm20) REVERT: C 256 ASN cc_start: 0.7996 (p0) cc_final: 0.7758 (p0) REVERT: C 292 GLN cc_start: 0.8423 (mt0) cc_final: 0.8148 (mt0) REVERT: C 425 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5670 (tp) REVERT: C 449 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8313 (tp) REVERT: C 538 MET cc_start: 0.7112 (mmm) cc_final: 0.6638 (mtp) REVERT: C 539 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7391 (mmt) REVERT: C 706 MET cc_start: 0.7000 (mtp) cc_final: 0.5661 (tpt) REVERT: C 824 PHE cc_start: 0.6948 (t80) cc_final: 0.6692 (t80) REVERT: C 844 LYS cc_start: 0.8688 (tttm) cc_final: 0.8192 (mmmt) REVERT: C 861 GLU cc_start: 0.8212 (tp30) cc_final: 0.7956 (tt0) REVERT: C 864 MET cc_start: 0.7885 (ttm) cc_final: 0.6844 (tpp) REVERT: C 893 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8162 (mmp) REVERT: C 907 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6595 (mm) outliers start: 92 outliers final: 35 residues processed: 324 average time/residue: 1.4657 time to fit residues: 540.2952 Evaluate side-chains 291 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 241 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 824 PHE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 963 ARG Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 963 ARG Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 893 MET Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 216 optimal weight: 0.0770 chunk 167 optimal weight: 0.0970 chunk 249 optimal weight: 0.0030 chunk 165 optimal weight: 0.0070 chunk 294 optimal weight: 0.5980 chunk 184 optimal weight: 0.4980 chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 469 GLN B 120 GLN B 534 HIS B 717 ASN B 805 GLN B 863 GLN C 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 24075 Z= 0.137 Angle : 0.541 12.007 32601 Z= 0.266 Chirality : 0.040 0.220 3879 Planarity : 0.004 0.044 4086 Dihedral : 6.141 58.790 3392 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.84 % Allowed : 20.69 % Favored : 76.47 % 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 (0.15), residues: 3063 helix: 0.36 (0.14), residues: 1590 sheet: -0.38 (0.22), residues: 513 loop : -0.91 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 886 HIS 0.006 0.001 HIS B 534 PHE 0.018 0.001 PHE A 824 TYR 0.011 0.001 TYR C 883 ARG 0.008 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 279 time to evaluate : 2.855 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5999 (mmm) cc_final: 0.5531 (mpp) REVERT: A 68 GLU cc_start: 0.7785 (mp0) cc_final: 0.7454 (mp0) REVERT: A 89 GLU cc_start: 0.7586 (tt0) cc_final: 0.7293 (tp30) REVERT: A 120 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8337 (mm110) REVERT: A 128 GLN cc_start: 0.7234 (mp10) cc_final: 0.6935 (mp10) REVERT: A 529 LEU cc_start: 0.8683 (tp) cc_final: 0.8276 (mm) REVERT: A 539 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7598 (mmp) REVERT: A 590 GLN cc_start: 0.7661 (tp40) cc_final: 0.7173 (tp-100) REVERT: A 637 SER cc_start: 0.7958 (t) cc_final: 0.7504 (m) REVERT: A 649 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7859 (p0) REVERT: A 695 MET cc_start: 0.8299 (tpp) cc_final: 0.7928 (mmt) REVERT: A 783 MET cc_start: 0.9040 (tpt) cc_final: 0.8767 (tpp) REVERT: A 844 LYS cc_start: 0.8575 (tttm) cc_final: 0.8151 (mppt) REVERT: A 888 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7229 (tt) REVERT: A 893 MET cc_start: 0.8429 (mmp) cc_final: 0.8223 (mmp) REVERT: A 963 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7701 (ttt180) REVERT: B 1 MET cc_start: 0.5967 (mmm) cc_final: 0.4946 (mpp) REVERT: B 4 PHE cc_start: 0.8318 (t80) cc_final: 0.8033 (t80) REVERT: B 128 GLN cc_start: 0.7222 (mp10) cc_final: 0.6998 (mp10) REVERT: B 353 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7669 (mp) REVERT: B 553 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7721 (mmp) REVERT: B 637 SER cc_start: 0.7987 (t) cc_final: 0.7568 (m) REVERT: B 695 MET cc_start: 0.7987 (mpp) cc_final: 0.7689 (mmt) REVERT: B 844 LYS cc_start: 0.8624 (tttm) cc_final: 0.8340 (mmpt) REVERT: B 963 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7716 (ttt-90) REVERT: C 256 ASN cc_start: 0.7985 (p0) cc_final: 0.7748 (p0) REVERT: C 292 GLN cc_start: 0.8403 (mt0) cc_final: 0.8088 (mt0) REVERT: C 353 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7604 (mp) REVERT: C 425 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.5725 (tp) REVERT: C 529 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8023 (mm) REVERT: C 538 MET cc_start: 0.6942 (mmm) cc_final: 0.6592 (mtp) REVERT: C 539 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7554 (mmt) REVERT: C 824 PHE cc_start: 0.6752 (t80) cc_final: 0.6515 (t80) REVERT: C 844 LYS cc_start: 0.8655 (tttm) cc_final: 0.8335 (mmpt) REVERT: C 861 GLU cc_start: 0.8341 (tp30) cc_final: 0.7777 (tt0) REVERT: C 864 MET cc_start: 0.7828 (ttm) cc_final: 0.6750 (tpp) REVERT: C 907 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6705 (mm) outliers start: 73 outliers final: 25 residues processed: 336 average time/residue: 1.4330 time to fit residues: 551.0991 Evaluate side-chains 288 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 251 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 963 ARG Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 963 ARG Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 88 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 268 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 534 HIS C 108 GLN C 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24075 Z= 0.198 Angle : 0.571 12.718 32601 Z= 0.279 Chirality : 0.041 0.208 3879 Planarity : 0.004 0.043 4086 Dihedral : 6.116 55.857 3392 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.49 % Allowed : 21.47 % Favored : 76.04 % 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: -0.15 (0.15), residues: 3063 helix: 0.50 (0.14), residues: 1587 sheet: -0.37 (0.22), residues: 543 loop : -0.76 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 886 HIS 0.006 0.001 HIS B 534 PHE 0.018 0.001 PHE B 824 TYR 0.016 0.001 TYR C 883 ARG 0.008 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 259 time to evaluate : 2.836 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6096 (mmm) cc_final: 0.5657 (mpp) REVERT: A 68 GLU cc_start: 0.7858 (mp0) cc_final: 0.7571 (mp0) REVERT: A 89 GLU cc_start: 0.7630 (tt0) cc_final: 0.7328 (tp30) REVERT: A 120 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8264 (mm110) REVERT: A 128 GLN cc_start: 0.7245 (mp10) cc_final: 0.6950 (mp10) REVERT: A 529 LEU cc_start: 0.8712 (tp) cc_final: 0.8434 (mm) REVERT: A 539 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7561 (mmt) REVERT: A 590 GLN cc_start: 0.7675 (tp40) cc_final: 0.7158 (tp-100) REVERT: A 637 SER cc_start: 0.8017 (t) cc_final: 0.7541 (m) REVERT: A 639 MET cc_start: 0.7972 (mtm) cc_final: 0.7584 (mtm) REVERT: A 649 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7831 (p0) REVERT: A 656 MET cc_start: 0.8173 (tpt) cc_final: 0.7778 (tpt) REVERT: A 783 MET cc_start: 0.9028 (tpt) cc_final: 0.8747 (tpp) REVERT: A 844 LYS cc_start: 0.8561 (tttm) cc_final: 0.8146 (mppt) REVERT: A 888 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7219 (tt) REVERT: A 963 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7669 (ttt180) REVERT: B 1 MET cc_start: 0.6086 (mmm) cc_final: 0.5089 (mpp) REVERT: B 4 PHE cc_start: 0.8313 (t80) cc_final: 0.7882 (t80) REVERT: B 128 GLN cc_start: 0.7259 (mp10) cc_final: 0.7001 (mp10) REVERT: B 353 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7676 (mp) REVERT: B 472 LEU cc_start: 0.8579 (tp) cc_final: 0.8362 (tp) REVERT: B 539 MET cc_start: 0.7863 (tpt) cc_final: 0.7584 (mmp) REVERT: B 553 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7718 (mmp) REVERT: B 637 SER cc_start: 0.8048 (t) cc_final: 0.7612 (m) REVERT: B 824 PHE cc_start: 0.7119 (p90) cc_final: 0.6885 (p90) REVERT: B 844 LYS cc_start: 0.8579 (tttm) cc_final: 0.8324 (mmpt) REVERT: B 861 GLU cc_start: 0.8416 (tp30) cc_final: 0.8085 (tt0) REVERT: B 963 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7832 (ttt180) REVERT: C 67 ARG cc_start: 0.8325 (ptm-80) cc_final: 0.7796 (ptp-170) REVERT: C 102 MET cc_start: 0.7326 (mmt) cc_final: 0.6814 (mmm) REVERT: C 164 GLU cc_start: 0.8291 (pm20) cc_final: 0.7396 (pm20) REVERT: C 256 ASN cc_start: 0.8005 (p0) cc_final: 0.7764 (p0) REVERT: C 292 GLN cc_start: 0.8411 (mt0) cc_final: 0.8143 (mt0) REVERT: C 353 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7785 (mp) REVERT: C 425 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5699 (tp) REVERT: C 538 MET cc_start: 0.7051 (mmm) cc_final: 0.6655 (mtp) REVERT: C 539 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7617 (mmt) REVERT: C 639 MET cc_start: 0.7710 (mtm) cc_final: 0.7397 (mtm) REVERT: C 824 PHE cc_start: 0.6829 (t80) cc_final: 0.6566 (t80) REVERT: C 844 LYS cc_start: 0.8641 (tttm) cc_final: 0.8335 (mmpt) REVERT: C 861 GLU cc_start: 0.8321 (tp30) cc_final: 0.7868 (tt0) REVERT: C 864 MET cc_start: 0.7871 (ttm) cc_final: 0.6780 (tpp) REVERT: C 907 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6651 (mm) outliers start: 64 outliers final: 35 residues processed: 314 average time/residue: 1.3753 time to fit residues: 494.7111 Evaluate side-chains 299 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 253 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 963 ARG Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 963 ARG Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 0.6980 chunk 257 optimal weight: 0.9980 chunk 274 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 273 optimal weight: 0.5980 chunk 180 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 534 HIS C 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24075 Z= 0.191 Angle : 0.574 12.545 32601 Z= 0.279 Chirality : 0.041 0.207 3879 Planarity : 0.004 0.042 4086 Dihedral : 6.041 54.123 3392 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.57 % Allowed : 21.24 % Favored : 76.20 % 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: -0.03 (0.16), residues: 3063 helix: 0.62 (0.14), residues: 1587 sheet: -0.28 (0.22), residues: 543 loop : -0.75 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 886 HIS 0.006 0.001 HIS B 534 PHE 0.016 0.001 PHE B 824 TYR 0.015 0.001 TYR B 883 ARG 0.008 0.000 ARG C 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 254 time to evaluate : 2.802 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6412 (mmm) cc_final: 0.5962 (mpp) REVERT: A 68 GLU cc_start: 0.7812 (mp0) cc_final: 0.7542 (mp0) REVERT: A 89 GLU cc_start: 0.7632 (tt0) cc_final: 0.7329 (tp30) REVERT: A 120 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8162 (mm110) REVERT: A 128 GLN cc_start: 0.7256 (mp10) cc_final: 0.6960 (mp10) REVERT: A 529 LEU cc_start: 0.8735 (tp) cc_final: 0.8477 (mm) REVERT: A 530 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7619 (tttt) REVERT: A 539 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7617 (mmt) REVERT: A 590 GLN cc_start: 0.7674 (tp40) cc_final: 0.7165 (tp-100) REVERT: A 637 SER cc_start: 0.7998 (t) cc_final: 0.7520 (m) REVERT: A 639 MET cc_start: 0.7962 (mtm) cc_final: 0.7581 (mtm) REVERT: A 649 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7764 (p0) REVERT: A 656 MET cc_start: 0.8140 (tpt) cc_final: 0.7713 (tpt) REVERT: A 695 MET cc_start: 0.8337 (mpp) cc_final: 0.7862 (mmt) REVERT: A 783 MET cc_start: 0.9047 (tpt) cc_final: 0.8759 (tpp) REVERT: A 844 LYS cc_start: 0.8553 (tttm) cc_final: 0.8147 (mppt) REVERT: A 888 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7213 (tt) REVERT: A 963 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7685 (ttt180) REVERT: B 1 MET cc_start: 0.6150 (mmm) cc_final: 0.5158 (mpp) REVERT: B 4 PHE cc_start: 0.8295 (t80) cc_final: 0.7869 (t80) REVERT: B 128 GLN cc_start: 0.7266 (mp10) cc_final: 0.7007 (mp10) REVERT: B 353 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7674 (mp) REVERT: B 472 LEU cc_start: 0.8575 (tp) cc_final: 0.8352 (tp) REVERT: B 539 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7565 (mmp) REVERT: B 553 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7752 (mmp) REVERT: B 637 SER cc_start: 0.8042 (t) cc_final: 0.7615 (m) REVERT: B 695 MET cc_start: 0.8085 (mpp) cc_final: 0.7798 (mmt) REVERT: B 706 MET cc_start: 0.6825 (mtp) cc_final: 0.5617 (tpt) REVERT: B 824 PHE cc_start: 0.7211 (p90) cc_final: 0.6992 (p90) REVERT: B 844 LYS cc_start: 0.8566 (tttm) cc_final: 0.8325 (mmpt) REVERT: B 861 GLU cc_start: 0.8372 (tp30) cc_final: 0.8068 (tt0) REVERT: B 883 TYR cc_start: 0.8029 (m-80) cc_final: 0.7514 (m-80) REVERT: B 908 MET cc_start: 0.8597 (mtt) cc_final: 0.8306 (mtt) REVERT: B 963 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7804 (ttt180) REVERT: C 4 PHE cc_start: 0.8258 (t80) cc_final: 0.7785 (t80) REVERT: C 67 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7819 (ptp-170) REVERT: C 102 MET cc_start: 0.7318 (mmt) cc_final: 0.6827 (mmm) REVERT: C 164 GLU cc_start: 0.8303 (pm20) cc_final: 0.7351 (pm20) REVERT: C 256 ASN cc_start: 0.8003 (p0) cc_final: 0.7756 (p0) REVERT: C 292 GLN cc_start: 0.8398 (mt0) cc_final: 0.8132 (mt0) REVERT: C 425 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5679 (tp) REVERT: C 529 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8028 (mm) REVERT: C 538 MET cc_start: 0.7054 (mmm) cc_final: 0.6610 (mtp) REVERT: C 539 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7595 (mmt) REVERT: C 639 MET cc_start: 0.7683 (mtm) cc_final: 0.7382 (mtm) REVERT: C 706 MET cc_start: 0.6901 (ttm) cc_final: 0.6556 (ptp) REVERT: C 824 PHE cc_start: 0.6821 (t80) cc_final: 0.6572 (t80) REVERT: C 844 LYS cc_start: 0.8629 (tttm) cc_final: 0.8289 (mmpt) REVERT: C 861 GLU cc_start: 0.8309 (tp30) cc_final: 0.7812 (tt0) REVERT: C 864 MET cc_start: 0.7880 (ttm) cc_final: 0.6770 (tpp) REVERT: C 907 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6624 (mm) outliers start: 66 outliers final: 37 residues processed: 308 average time/residue: 1.4443 time to fit residues: 509.7358 Evaluate side-chains 301 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 250 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 963 ARG Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 963 ARG Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 280 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 534 HIS C 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24075 Z= 0.213 Angle : 0.589 12.693 32601 Z= 0.287 Chirality : 0.042 0.206 3879 Planarity : 0.004 0.042 4086 Dihedral : 6.050 56.594 3392 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.22 % Allowed : 21.78 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.02 (0.16), residues: 3063 helix: 0.66 (0.14), residues: 1587 sheet: -0.25 (0.22), residues: 543 loop : -0.74 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 886 HIS 0.007 0.001 HIS B 534 PHE 0.018 0.001 PHE B 866 TYR 0.020 0.001 TYR C 883 ARG 0.008 0.001 ARG C 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 261 time to evaluate : 2.715 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6424 (mmm) cc_final: 0.5952 (mpp) REVERT: A 67 ARG cc_start: 0.8226 (ptp-110) cc_final: 0.7811 (ptp-170) REVERT: A 68 GLU cc_start: 0.7912 (mp0) cc_final: 0.7384 (mp0) REVERT: A 89 GLU cc_start: 0.7639 (tt0) cc_final: 0.7334 (tp30) REVERT: A 120 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8104 (mm110) REVERT: A 128 GLN cc_start: 0.7271 (mp10) cc_final: 0.6970 (mp10) REVERT: A 509 PHE cc_start: 0.6834 (t80) cc_final: 0.6552 (OUTLIER) REVERT: A 529 LEU cc_start: 0.8740 (tp) cc_final: 0.8476 (mm) REVERT: A 539 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7583 (mmt) REVERT: A 590 GLN cc_start: 0.7676 (tp40) cc_final: 0.7163 (tp-100) REVERT: A 637 SER cc_start: 0.8062 (t) cc_final: 0.7564 (m) REVERT: A 639 MET cc_start: 0.7978 (mtm) cc_final: 0.7599 (mtm) REVERT: A 656 MET cc_start: 0.8169 (tpt) cc_final: 0.7823 (tpt) REVERT: A 695 MET cc_start: 0.8350 (mpp) cc_final: 0.7905 (mmt) REVERT: A 783 MET cc_start: 0.9038 (tpt) cc_final: 0.8750 (tpp) REVERT: A 844 LYS cc_start: 0.8534 (tttm) cc_final: 0.8137 (mppt) REVERT: A 888 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7187 (tt) REVERT: A 963 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7677 (ttt180) REVERT: B 1 MET cc_start: 0.6282 (mmm) cc_final: 0.5264 (mpp) REVERT: B 4 PHE cc_start: 0.8310 (t80) cc_final: 0.7894 (t80) REVERT: B 128 GLN cc_start: 0.7287 (mp10) cc_final: 0.7030 (mp10) REVERT: B 353 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7677 (mp) REVERT: B 472 LEU cc_start: 0.8574 (tp) cc_final: 0.8345 (tp) REVERT: B 539 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7607 (mmp) REVERT: B 553 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7836 (mmp) REVERT: B 637 SER cc_start: 0.7899 (t) cc_final: 0.7461 (m) REVERT: B 695 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7816 (mmt) REVERT: B 706 MET cc_start: 0.6786 (mtp) cc_final: 0.5638 (tpt) REVERT: B 756 GLN cc_start: 0.8537 (pt0) cc_final: 0.8299 (pt0) REVERT: B 844 LYS cc_start: 0.8585 (tttm) cc_final: 0.8347 (mmpt) REVERT: B 861 GLU cc_start: 0.8425 (tp30) cc_final: 0.7992 (tt0) REVERT: B 908 MET cc_start: 0.8597 (mtt) cc_final: 0.8373 (mtt) REVERT: B 963 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7801 (ttt180) REVERT: C 4 PHE cc_start: 0.8248 (t80) cc_final: 0.7801 (t80) REVERT: C 67 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7764 (ptp-170) REVERT: C 102 MET cc_start: 0.7285 (mmt) cc_final: 0.6641 (mmm) REVERT: C 164 GLU cc_start: 0.8275 (pm20) cc_final: 0.7347 (pm20) REVERT: C 256 ASN cc_start: 0.8004 (p0) cc_final: 0.7777 (p0) REVERT: C 292 GLN cc_start: 0.8422 (mt0) cc_final: 0.8162 (mt0) REVERT: C 425 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5537 (tp) REVERT: C 529 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8028 (mm) REVERT: C 538 MET cc_start: 0.7078 (mmm) cc_final: 0.6614 (mtp) REVERT: C 539 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7586 (mmt) REVERT: C 639 MET cc_start: 0.7689 (mtm) cc_final: 0.7411 (mtm) REVERT: C 706 MET cc_start: 0.6898 (ttm) cc_final: 0.6591 (ptp) REVERT: C 824 PHE cc_start: 0.6838 (t80) cc_final: 0.6607 (t80) REVERT: C 844 LYS cc_start: 0.8625 (tttm) cc_final: 0.8293 (mmpt) REVERT: C 861 GLU cc_start: 0.8277 (tp30) cc_final: 0.7699 (tt0) REVERT: C 864 MET cc_start: 0.7898 (ttm) cc_final: 0.6779 (tpp) REVERT: C 907 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6588 (mm) outliers start: 57 outliers final: 38 residues processed: 306 average time/residue: 1.4493 time to fit residues: 505.5930 Evaluate side-chains 304 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 254 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 692 ASP Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 963 ARG Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 600 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 963 ARG Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 600 ASP Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 702 LYS Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 1012 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 249 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 534 HIS C 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.116005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090048 restraints weight = 38680.863| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.25 r_work: 0.3041 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24075 Z= 0.220 Angle : 0.591 12.698 32601 Z= 0.289 Chirality : 0.042 0.206 3879 Planarity : 0.004 0.041 4086 Dihedral : 6.059 57.680 3392 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.41 % Allowed : 22.05 % Favored : 75.53 % 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: 0.01 (0.16), residues: 3063 helix: 0.68 (0.14), residues: 1590 sheet: -0.23 (0.22), residues: 543 loop : -0.81 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 556 HIS 0.007 0.001 HIS B 534 PHE 0.018 0.001 PHE B 866 TYR 0.025 0.001 TYR C 883 ARG 0.008 0.001 ARG B 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9141.76 seconds wall clock time: 163 minutes 33.62 seconds (9813.62 seconds total)