Starting phenix.real_space_refine on Fri Mar 15 04:39:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7j_9935/03_2024/6k7j_9935.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7j_9935/03_2024/6k7j_9935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7j_9935/03_2024/6k7j_9935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7j_9935/03_2024/6k7j_9935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7j_9935/03_2024/6k7j_9935.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7j_9935/03_2024/6k7j_9935.pdb" } resolution = 3.08 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 56 5.16 5 C 6863 2.51 5 N 1757 2.21 5 O 1922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 786": "OD1" <-> "OD2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7853 Classifications: {'peptide': 986} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 955} Chain breaks: 3 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.48, per 1000 atoms: 0.61 Number of scatterers: 10602 At special positions: 0 Unit cell: (73.87, 116.2, 166.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 3 15.00 Mg 1 11.99 O 1922 8.00 N 1757 7.00 C 6863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.05 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 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 4.43 Conformation dependent library (CDL) restraints added in 1.9 seconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 46.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.985A pdb=" N TYR A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 123 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.825A pdb=" N MET A 180 " --> pdb=" O PRO A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 288 through 323 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.266A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 397 " --> pdb=" O SER A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 398 through 401 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.810A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 500 Processing helix chain 'A' and resid 559 through 565 removed outlier: 3.606A pdb=" N ASP A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 removed outlier: 5.120A pdb=" N ILE A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 615 removed outlier: 4.635A pdb=" N GLU A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 633 removed outlier: 3.545A pdb=" N LEU A 625 " --> pdb=" O ARG A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 730 through 738 removed outlier: 4.143A pdb=" N TYR A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 753 Processing helix chain 'A' and resid 762 through 778 removed outlier: 4.191A pdb=" N GLN A 776 " --> pdb=" O MET A 772 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS A 778 " --> pdb=" O LYS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 823 through 831 removed outlier: 4.337A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 866 removed outlier: 4.313A pdb=" N ILE A 857 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE A 859 " --> pdb=" O TYR A 855 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 881 Processing helix chain 'A' and resid 887 through 896 removed outlier: 4.134A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.756A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 917' Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 985 removed outlier: 4.115A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1020 through 1024 Processing helix chain 'A' and resid 1025 through 1033 Processing helix chain 'A' and resid 1035 through 1062 removed outlier: 4.145A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 5.196A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 74 removed outlier: 3.919A pdb=" N LEU C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.736A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 removed outlier: 4.019A pdb=" N ILE C 253 " --> pdb=" O ASN C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 253' Processing helix chain 'C' and resid 254 through 262 removed outlier: 3.688A pdb=" N ARG C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137 removed outlier: 4.339A pdb=" N GLN A 136 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 158 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASP A 168 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 184 removed outlier: 3.904A pdb=" N CYS A 181 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.542A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL A 403 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU A 782 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR A 405 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE A 784 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A 407 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU A 669 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER A 408 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.620A pdb=" N VAL A 429 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS A 424 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 641 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 592 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 508 removed outlier: 3.516A pdb=" N VAL A 515 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 518 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 81 removed outlier: 5.881A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.291A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.291A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 162 through 163 468 hydrogen bonds defined for protein. 1344 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: 3.65 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1885 1.32 - 1.45: 2830 1.45 - 1.57: 6044 1.57 - 1.69: 6 1.69 - 1.82: 87 Bond restraints: 10852 Sorted by residual: bond pdb=" O2B ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sigma weight residual 1.507 1.607 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O3A ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sigma weight residual 1.698 1.606 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C4 ACP A1201 " pdb=" C5 ACP A1201 " ideal model delta sigma weight residual 1.386 1.465 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3G ACP A1201 " pdb=" PG ACP A1201 " ideal model delta sigma weight residual 1.532 1.605 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CD LYS C 308 " pdb=" CE LYS C 308 " ideal model delta sigma weight residual 1.520 1.413 0.107 3.00e-02 1.11e+03 1.28e+01 ... (remaining 10847 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.52: 222 105.52 - 113.13: 5794 113.13 - 120.73: 5114 120.73 - 128.34: 3503 128.34 - 135.95: 104 Bond angle restraints: 14737 Sorted by residual: angle pdb=" N ASP A 672 " pdb=" CA ASP A 672 " pdb=" C ASP A 672 " ideal model delta sigma weight residual 113.18 120.61 -7.43 1.33e+00 5.65e-01 3.12e+01 angle pdb=" C PRO A 91 " pdb=" N ASP A 92 " pdb=" CA ASP A 92 " ideal model delta sigma weight residual 121.54 132.00 -10.46 1.91e+00 2.74e-01 3.00e+01 angle pdb=" CA LEU A 738 " pdb=" CB LEU A 738 " pdb=" CG LEU A 738 " ideal model delta sigma weight residual 116.30 133.58 -17.28 3.50e+00 8.16e-02 2.44e+01 angle pdb=" C LYS A 483 " pdb=" N ILE A 484 " pdb=" CA ILE A 484 " ideal model delta sigma weight residual 121.97 130.59 -8.62 1.80e+00 3.09e-01 2.30e+01 angle pdb=" N VAL A 742 " pdb=" CA VAL A 742 " pdb=" C VAL A 742 " ideal model delta sigma weight residual 111.91 107.98 3.93 8.90e-01 1.26e+00 1.95e+01 ... (remaining 14732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.36: 6367 32.36 - 64.72: 203 64.72 - 97.08: 14 97.08 - 129.43: 0 129.43 - 161.79: 2 Dihedral angle restraints: 6586 sinusoidal: 2760 harmonic: 3826 Sorted by residual: dihedral pdb=" CA ALA A1020 " pdb=" C ALA A1020 " pdb=" N PRO A1021 " pdb=" CA PRO A1021 " ideal model delta harmonic sigma weight residual 180.00 -120.56 -59.44 0 5.00e+00 4.00e-02 1.41e+02 dihedral pdb=" CA THR A 511 " pdb=" C THR A 511 " pdb=" N PRO A 512 " pdb=" CA PRO A 512 " ideal model delta harmonic sigma weight residual 180.00 128.89 51.11 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA LEU C 243 " pdb=" C LEU C 243 " pdb=" N ASP C 244 " pdb=" CA ASP C 244 " ideal model delta harmonic sigma weight residual 180.00 146.95 33.05 0 5.00e+00 4.00e-02 4.37e+01 ... (remaining 6583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1313 0.081 - 0.162: 321 0.162 - 0.243: 46 0.243 - 0.324: 1 0.324 - 0.405: 3 Chirality restraints: 1684 Sorted by residual: chirality pdb=" C4 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C5 NAG B 2 " pdb=" O4 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.13 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CB ILE A 219 " pdb=" CA ILE A 219 " pdb=" CG1 ILE A 219 " pdb=" CG2 ILE A 219 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CG LEU A 964 " pdb=" CB LEU A 964 " pdb=" CD1 LEU A 964 " pdb=" CD2 LEU A 964 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1681 not shown) Planarity restraints: 1838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.351 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG B 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " 0.270 2.00e-02 2.50e+03 2.29e-01 6.58e+02 pdb=" C7 NAG C 402 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " -0.394 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.230 2.00e-02 2.50e+03 1.95e-01 4.74e+02 pdb=" C7 NAG C 401 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.156 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.330 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.001 2.00e-02 2.50e+03 ... (remaining 1835 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 479 2.71 - 3.26: 9883 3.26 - 3.80: 17417 3.80 - 4.35: 22588 4.35 - 4.90: 37953 Nonbonded interactions: 88320 Sorted by model distance: nonbonded pdb=" OD2 ASP A 409 " pdb="MG MG A1202 " model vdw 2.159 2.170 nonbonded pdb=" O TYR A 881 " pdb=" OG1 THR A 886 " model vdw 2.244 2.440 nonbonded pdb=" OH TYR C 134 " pdb=" OG SER C 177 " model vdw 2.245 2.440 nonbonded pdb=" O GLU A 222 " pdb=" OH TYR A 269 " model vdw 2.263 2.440 nonbonded pdb=" O CYS A 50 " pdb=" OG1 THR A 270 " model vdw 2.278 2.440 ... (remaining 88315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.990 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 32.650 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.013 0.125 10852 Z= 0.831 Angle : 1.229 17.279 14737 Z= 0.645 Chirality : 0.071 0.405 1684 Planarity : 0.014 0.300 1835 Dihedral : 15.542 161.793 4109 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.61 % Favored : 91.24 % Rotamer: Outliers : 0.17 % Allowed : 9.12 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.08 % 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: -3.98 (0.18), residues: 1301 helix: -2.61 (0.16), residues: 577 sheet: -1.21 (0.39), residues: 156 loop : -3.03 (0.21), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP A 927 HIS 0.009 0.002 HIS A 323 PHE 0.045 0.004 PHE C 304 TYR 0.025 0.003 TYR C 122 ARG 0.017 0.001 ARG A 898 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.201 Fit side-chains REVERT: A 155 ASP cc_start: 0.5940 (m-30) cc_final: 0.5620 (m-30) REVERT: A 178 GLN cc_start: 0.7103 (tm-30) cc_final: 0.6888 (tm-30) REVERT: A 419 MET cc_start: 0.7777 (mtt) cc_final: 0.7516 (mtt) REVERT: A 645 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6531 (mt-10) REVERT: A 665 LYS cc_start: 0.7853 (mttt) cc_final: 0.7102 (mmtt) REVERT: A 904 ASN cc_start: 0.8244 (m110) cc_final: 0.7983 (m110) REVERT: A 1058 LYS cc_start: 0.6492 (mmmt) cc_final: 0.6280 (mtpt) REVERT: A 1059 ARG cc_start: 0.6166 (tmt-80) cc_final: 0.5784 (ttt-90) REVERT: C 49 THR cc_start: 0.8321 (m) cc_final: 0.8093 (p) REVERT: C 215 ARG cc_start: 0.7270 (mtt90) cc_final: 0.6997 (mmp-170) REVERT: C 290 ARG cc_start: 0.7336 (ttt-90) cc_final: 0.6916 (mtp-110) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.2486 time to fit residues: 44.9404 Evaluate side-chains 102 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 0.0270 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 51 ASN A 78 ASN A 124 HIS A 128 ASN A 136 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 261 GLN A 381 HIS A 397 ASN ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10852 Z= 0.188 Angle : 0.662 9.171 14737 Z= 0.341 Chirality : 0.045 0.189 1684 Planarity : 0.006 0.086 1835 Dihedral : 10.366 160.366 1622 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.30 % Favored : 93.54 % Rotamer: Outliers : 1.82 % Allowed : 11.29 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.61 (0.21), residues: 1301 helix: -1.06 (0.19), residues: 587 sheet: -1.10 (0.37), residues: 169 loop : -2.64 (0.23), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.016 0.001 PHE A 368 TYR 0.016 0.001 TYR C 121 ARG 0.003 0.000 ARG A 898 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 155 ASP cc_start: 0.5944 (m-30) cc_final: 0.5649 (m-30) REVERT: A 225 ASN cc_start: 0.6614 (t0) cc_final: 0.6291 (t0) REVERT: A 645 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6726 (mt-10) REVERT: A 665 LYS cc_start: 0.8029 (mttt) cc_final: 0.7178 (mmtt) REVERT: A 778 LYS cc_start: 0.7530 (mptt) cc_final: 0.7236 (mmtp) REVERT: A 874 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: A 904 ASN cc_start: 0.8128 (m110) cc_final: 0.7818 (m110) REVERT: A 1059 ARG cc_start: 0.6078 (tmt-80) cc_final: 0.5699 (ttt-90) REVERT: C 155 LYS cc_start: 0.8103 (mptt) cc_final: 0.7626 (mmmt) REVERT: C 215 ARG cc_start: 0.7101 (mtt90) cc_final: 0.6819 (mmp-170) REVERT: C 290 ARG cc_start: 0.7031 (ttt-90) cc_final: 0.6786 (mtm180) outliers start: 21 outliers final: 10 residues processed: 128 average time/residue: 0.2388 time to fit residues: 42.9568 Evaluate side-chains 110 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 98 optimal weight: 0.0570 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 overall best weight: 1.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 453 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10852 Z= 0.279 Angle : 0.661 9.265 14737 Z= 0.339 Chirality : 0.046 0.223 1684 Planarity : 0.006 0.089 1835 Dihedral : 9.939 155.973 1621 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.76 % Favored : 93.08 % Rotamer: Outliers : 2.87 % Allowed : 14.16 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.98 (0.22), residues: 1301 helix: -0.49 (0.20), residues: 582 sheet: -0.81 (0.38), residues: 173 loop : -2.38 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 927 HIS 0.004 0.001 HIS A 124 PHE 0.021 0.002 PHE C 304 TYR 0.013 0.001 TYR C 121 ARG 0.002 0.000 ARG A 898 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.5992 (m-30) cc_final: 0.5728 (m-30) REVERT: A 225 ASN cc_start: 0.6578 (t0) cc_final: 0.6291 (t0) REVERT: A 645 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6452 (mt-10) REVERT: A 665 LYS cc_start: 0.8044 (mttt) cc_final: 0.7273 (mmtm) REVERT: A 874 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: A 904 ASN cc_start: 0.8121 (m110) cc_final: 0.7531 (m110) REVERT: A 1059 ARG cc_start: 0.6166 (tmt-80) cc_final: 0.5712 (ttt-90) REVERT: C 155 LYS cc_start: 0.8115 (mptt) cc_final: 0.7648 (mmmt) REVERT: C 185 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 215 ARG cc_start: 0.7144 (mtt90) cc_final: 0.6883 (mmp-170) REVERT: C 290 ARG cc_start: 0.6987 (ttt-90) cc_final: 0.6730 (mtm180) outliers start: 33 outliers final: 19 residues processed: 132 average time/residue: 0.2280 time to fit residues: 43.4991 Evaluate side-chains 118 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10852 Z= 0.195 Angle : 0.598 8.211 14737 Z= 0.308 Chirality : 0.044 0.192 1684 Planarity : 0.005 0.080 1835 Dihedral : 9.428 151.297 1621 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 2.35 % Allowed : 15.81 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.53 (0.22), residues: 1301 helix: -0.10 (0.21), residues: 587 sheet: -0.53 (0.39), residues: 172 loop : -2.19 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.015 0.001 PHE A 368 TYR 0.012 0.001 TYR C 121 ARG 0.001 0.000 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.6086 (m-30) cc_final: 0.5876 (m-30) REVERT: A 225 ASN cc_start: 0.6501 (t0) cc_final: 0.6295 (t0) REVERT: A 493 GLU cc_start: 0.5757 (mt-10) cc_final: 0.5443 (mt-10) REVERT: A 645 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6435 (mt-10) REVERT: A 665 LYS cc_start: 0.8017 (mttt) cc_final: 0.7326 (mmtm) REVERT: A 874 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7053 (tp30) REVERT: A 904 ASN cc_start: 0.8142 (m110) cc_final: 0.7902 (m110) REVERT: A 1058 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6197 (ttmt) REVERT: A 1059 ARG cc_start: 0.6092 (tmt-80) cc_final: 0.5663 (ttt-90) REVERT: C 155 LYS cc_start: 0.8023 (mptt) cc_final: 0.7564 (mmmt) REVERT: C 215 ARG cc_start: 0.7104 (mtt90) cc_final: 0.6848 (mmp-170) REVERT: C 290 ARG cc_start: 0.6937 (ttt-90) cc_final: 0.6681 (mtm180) outliers start: 27 outliers final: 16 residues processed: 125 average time/residue: 0.2286 time to fit residues: 41.4602 Evaluate side-chains 115 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10852 Z= 0.245 Angle : 0.613 8.709 14737 Z= 0.313 Chirality : 0.045 0.204 1684 Planarity : 0.005 0.084 1835 Dihedral : 9.291 148.630 1621 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.30 % Favored : 93.54 % Rotamer: Outliers : 3.04 % Allowed : 16.07 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.34 (0.23), residues: 1301 helix: 0.08 (0.21), residues: 579 sheet: -0.39 (0.39), residues: 172 loop : -2.12 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.004 0.001 HIS A 124 PHE 0.016 0.001 PHE A 368 TYR 0.012 0.001 TYR C 121 ARG 0.002 0.000 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.6143 (m-30) cc_final: 0.5906 (m-30) REVERT: A 225 ASN cc_start: 0.6596 (t0) cc_final: 0.6275 (t0) REVERT: A 645 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6725 (mt-10) REVERT: A 665 LYS cc_start: 0.8021 (mttt) cc_final: 0.7351 (mmtm) REVERT: A 874 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7071 (tp30) REVERT: A 904 ASN cc_start: 0.8232 (m110) cc_final: 0.7939 (m110) REVERT: A 1059 ARG cc_start: 0.6119 (tmt-80) cc_final: 0.5655 (ttt-90) REVERT: C 155 LYS cc_start: 0.8056 (mptt) cc_final: 0.7569 (mmmt) REVERT: C 185 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8379 (mp) REVERT: C 215 ARG cc_start: 0.7167 (mtt90) cc_final: 0.6923 (mmp-170) REVERT: C 290 ARG cc_start: 0.6871 (ttt-90) cc_final: 0.6567 (mtm180) outliers start: 35 outliers final: 24 residues processed: 131 average time/residue: 0.2331 time to fit residues: 44.0998 Evaluate side-chains 125 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 104 optimal weight: 0.0970 chunk 58 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10852 Z= 0.242 Angle : 0.606 10.897 14737 Z= 0.308 Chirality : 0.045 0.202 1684 Planarity : 0.005 0.080 1835 Dihedral : 9.109 145.464 1621 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.61 % Favored : 94.24 % Rotamer: Outliers : 3.13 % Allowed : 17.03 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.23 (0.23), residues: 1301 helix: 0.16 (0.21), residues: 580 sheet: -0.29 (0.40), residues: 172 loop : -2.06 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.004 0.001 HIS A 124 PHE 0.016 0.001 PHE C 304 TYR 0.013 0.001 TYR C 121 ARG 0.002 0.000 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 100 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.6145 (m-30) cc_final: 0.5889 (m-30) REVERT: A 225 ASN cc_start: 0.6608 (t0) cc_final: 0.6289 (t0) REVERT: A 645 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6567 (mt-10) REVERT: A 665 LYS cc_start: 0.8012 (mttt) cc_final: 0.7354 (mmtm) REVERT: A 874 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7278 (tp30) REVERT: A 904 ASN cc_start: 0.8233 (m110) cc_final: 0.7904 (m110) REVERT: A 1059 ARG cc_start: 0.6149 (tmt-80) cc_final: 0.5674 (ttt-90) REVERT: C 115 GLU cc_start: 0.8072 (pt0) cc_final: 0.7743 (pt0) REVERT: C 155 LYS cc_start: 0.8016 (mptt) cc_final: 0.7535 (mmmt) REVERT: C 185 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8358 (mp) REVERT: C 215 ARG cc_start: 0.7137 (mtt90) cc_final: 0.6879 (mmp-170) REVERT: C 290 ARG cc_start: 0.6864 (ttt-90) cc_final: 0.6574 (mtm180) outliers start: 36 outliers final: 27 residues processed: 131 average time/residue: 0.2138 time to fit residues: 40.8742 Evaluate side-chains 128 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10852 Z= 0.220 Angle : 0.589 8.624 14737 Z= 0.300 Chirality : 0.044 0.195 1684 Planarity : 0.005 0.080 1835 Dihedral : 8.972 143.027 1621 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.85 % Rotamer: Outliers : 3.30 % Allowed : 17.38 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.12 (0.23), residues: 1301 helix: 0.27 (0.21), residues: 582 sheet: -0.51 (0.38), residues: 192 loop : -1.98 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.004 0.001 HIS A 124 PHE 0.015 0.001 PHE C 304 TYR 0.012 0.001 TYR C 121 ARG 0.001 0.000 ARG A 898 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 102 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.6028 (m-30) cc_final: 0.5821 (m-30) REVERT: A 225 ASN cc_start: 0.6565 (t0) cc_final: 0.6257 (t0) REVERT: A 493 GLU cc_start: 0.5810 (mt-10) cc_final: 0.5451 (mt-10) REVERT: A 645 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6508 (mt-10) REVERT: A 665 LYS cc_start: 0.8032 (mttt) cc_final: 0.7403 (mmtm) REVERT: A 874 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7252 (tp30) REVERT: A 904 ASN cc_start: 0.8238 (m110) cc_final: 0.7878 (m110) REVERT: A 1059 ARG cc_start: 0.6117 (tmt-80) cc_final: 0.5674 (ttt-90) REVERT: C 115 GLU cc_start: 0.8060 (pt0) cc_final: 0.7837 (pt0) REVERT: C 155 LYS cc_start: 0.7996 (mptt) cc_final: 0.7519 (mmmt) REVERT: C 215 ARG cc_start: 0.7144 (mtt90) cc_final: 0.6888 (mmp-170) REVERT: C 290 ARG cc_start: 0.6846 (ttt-90) cc_final: 0.6540 (mtm110) outliers start: 38 outliers final: 28 residues processed: 135 average time/residue: 0.2196 time to fit residues: 42.8301 Evaluate side-chains 129 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 0.0470 chunk 79 optimal weight: 0.5980 chunk 85 optimal weight: 0.0070 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10852 Z= 0.144 Angle : 0.547 8.449 14737 Z= 0.280 Chirality : 0.042 0.182 1684 Planarity : 0.005 0.076 1835 Dihedral : 8.657 138.789 1621 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.30 % Favored : 94.54 % Rotamer: Outliers : 2.43 % Allowed : 18.42 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.85 (0.23), residues: 1301 helix: 0.55 (0.22), residues: 576 sheet: -0.19 (0.39), residues: 182 loop : -1.93 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.002 0.001 HIS A 323 PHE 0.014 0.001 PHE A 368 TYR 0.011 0.001 TYR C 121 ARG 0.002 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.6072 (m-30) cc_final: 0.5861 (m-30) REVERT: A 225 ASN cc_start: 0.6518 (t0) cc_final: 0.6257 (t0) REVERT: A 589 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5302 (mt) REVERT: A 645 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6379 (mt-10) REVERT: A 665 LYS cc_start: 0.7995 (mttt) cc_final: 0.7293 (mmtt) REVERT: A 685 LYS cc_start: 0.6259 (mttp) cc_final: 0.5107 (mmmt) REVERT: A 874 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: A 904 ASN cc_start: 0.8110 (m110) cc_final: 0.7335 (m110) REVERT: A 1058 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.6175 (ttmt) REVERT: A 1059 ARG cc_start: 0.6026 (tmt-80) cc_final: 0.5572 (ttt-90) REVERT: C 115 GLU cc_start: 0.7912 (pt0) cc_final: 0.7677 (pt0) REVERT: C 155 LYS cc_start: 0.7872 (mptt) cc_final: 0.7423 (mmmt) REVERT: C 215 ARG cc_start: 0.7056 (mtt90) cc_final: 0.6790 (mmp-170) REVERT: C 290 ARG cc_start: 0.6841 (ttt-90) cc_final: 0.6575 (mtm180) outliers start: 28 outliers final: 19 residues processed: 131 average time/residue: 0.2256 time to fit residues: 42.5878 Evaluate side-chains 119 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 0.1980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10852 Z= 0.179 Angle : 0.570 8.852 14737 Z= 0.289 Chirality : 0.043 0.175 1684 Planarity : 0.005 0.079 1835 Dihedral : 8.659 138.094 1621 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.61 % Favored : 94.24 % Rotamer: Outliers : 2.00 % Allowed : 18.85 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.87 (0.23), residues: 1301 helix: 0.48 (0.22), residues: 584 sheet: -0.30 (0.38), residues: 192 loop : -1.89 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.012 0.001 PHE C 304 TYR 0.012 0.001 TYR C 121 ARG 0.001 0.000 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.6083 (m-30) cc_final: 0.5875 (m-30) REVERT: A 225 ASN cc_start: 0.6468 (t0) cc_final: 0.6207 (t0) REVERT: A 589 LEU cc_start: 0.5631 (OUTLIER) cc_final: 0.5423 (mt) REVERT: A 645 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6375 (mt-10) REVERT: A 665 LYS cc_start: 0.8006 (mttt) cc_final: 0.7271 (mmtt) REVERT: A 685 LYS cc_start: 0.6274 (mttp) cc_final: 0.5124 (mmmt) REVERT: A 874 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7286 (tp30) REVERT: A 904 ASN cc_start: 0.8055 (m110) cc_final: 0.7673 (m-40) REVERT: A 1058 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.6142 (ttmt) REVERT: A 1059 ARG cc_start: 0.6058 (tmt-80) cc_final: 0.5592 (ttt-90) REVERT: C 215 ARG cc_start: 0.7083 (mtt90) cc_final: 0.6804 (mmp-170) REVERT: C 290 ARG cc_start: 0.6835 (ttt-90) cc_final: 0.6574 (mtm180) outliers start: 23 outliers final: 17 residues processed: 120 average time/residue: 0.2322 time to fit residues: 40.8327 Evaluate side-chains 119 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 4.9990 chunk 58 optimal weight: 30.0000 chunk 85 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 119 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10852 Z= 0.257 Angle : 0.609 9.135 14737 Z= 0.308 Chirality : 0.045 0.202 1684 Planarity : 0.005 0.080 1835 Dihedral : 8.809 138.421 1621 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.16 % Rotamer: Outliers : 2.26 % Allowed : 18.68 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.00 (0.23), residues: 1301 helix: 0.32 (0.21), residues: 583 sheet: -0.32 (0.38), residues: 192 loop : -1.91 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 876 HIS 0.005 0.001 HIS A 124 PHE 0.017 0.001 PHE C 304 TYR 0.013 0.001 TYR C 122 ARG 0.002 0.000 ARG A 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ASN cc_start: 0.6377 (t0) cc_final: 0.6121 (t0) REVERT: A 372 TYR cc_start: 0.7379 (m-80) cc_final: 0.7139 (m-10) REVERT: A 589 LEU cc_start: 0.5615 (OUTLIER) cc_final: 0.5401 (mt) REVERT: A 645 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6300 (mt-10) REVERT: A 665 LYS cc_start: 0.8022 (mttt) cc_final: 0.7352 (mmtm) REVERT: A 685 LYS cc_start: 0.6276 (mttp) cc_final: 0.5119 (mmmt) REVERT: A 874 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: A 904 ASN cc_start: 0.8080 (m110) cc_final: 0.7286 (m-40) REVERT: A 1059 ARG cc_start: 0.6156 (tmt-80) cc_final: 0.5662 (ttt-90) REVERT: C 215 ARG cc_start: 0.7170 (mtt90) cc_final: 0.6862 (mmp-170) REVERT: C 290 ARG cc_start: 0.6855 (ttt-90) cc_final: 0.6566 (mtm110) outliers start: 26 outliers final: 20 residues processed: 121 average time/residue: 0.2171 time to fit residues: 38.1503 Evaluate side-chains 118 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 1058 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.194861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.158734 restraints weight = 10199.031| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.96 r_work: 0.3289 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10852 Z= 0.213 Angle : 0.590 9.218 14737 Z= 0.299 Chirality : 0.044 0.185 1684 Planarity : 0.005 0.079 1835 Dihedral : 8.772 137.501 1621 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.16 % Rotamer: Outliers : 1.91 % Allowed : 19.03 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.93 (0.23), residues: 1301 helix: 0.38 (0.21), residues: 581 sheet: -0.29 (0.38), residues: 192 loop : -1.87 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.003 0.001 HIS A 124 PHE 0.014 0.001 PHE C 304 TYR 0.012 0.001 TYR C 121 ARG 0.001 0.000 ARG C 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2189.06 seconds wall clock time: 40 minutes 21.71 seconds (2421.71 seconds total)