Starting phenix.real_space_refine on Tue Nov 18 07:44:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s8j_10124/11_2025/6s8j_10124.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8j_10124/11_2025/6s8j_10124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6s8j_10124/11_2025/6s8j_10124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8j_10124/11_2025/6s8j_10124.map" model { file = "/net/cci-nas-00/data/ceres_data/6s8j_10124/11_2025/6s8j_10124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8j_10124/11_2025/6s8j_10124.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.194 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7728 2.51 5 N 2106 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12391 Number of models: 1 Model: "" Number of chains: 17 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 937 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Y" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Restraints were copied for chains: O, U, P, Y, C, E, D, F, I, J Time building chain proxies: 2.44, per 1000 atoms: 0.20 Number of scatterers: 12391 At special positions: 0 Unit cell: (99.333, 97.635, 122.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2500 8.00 N 2106 7.00 C 7728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS H 105 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=1.99 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 91 " distance=2.04 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 91 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 98 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 98 " distance=2.04 Simple disulfide: pdb=" SG CYS P 105 " - pdb=" SG CYS P 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 105 " - pdb=" SG CYS Y 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS D 609 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS F 609 " distance=2.08 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.04 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.04 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN D 563 " " NAG J 1 " - " ASN F 563 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 631.2 milliseconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2820 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 33 sheets defined 14.6% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.931A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.599A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.951A pdb=" N ILE B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.518A pdb=" N GLY B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.700A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.931A pdb=" N GLU O 86 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 86 removed outlier: 3.932A pdb=" N GLU U 86 " --> pdb=" O ALA U 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.951A pdb=" N ILE D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.518A pdb=" N GLY D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.700A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.951A pdb=" N ILE F 542 " --> pdb=" O ALA F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.518A pdb=" N GLY F 557 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.700A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.599A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 84 removed outlier: 3.599A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 53 through 57 Processing helix chain 'Y' and resid 28 through 32 Processing helix chain 'Y' and resid 53 through 57 Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.254A pdb=" N GLN L 40 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.614A pdb=" N GLN L 101 " --> pdb=" O ASP L 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 60 through 62 removed outlier: 5.168A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.705A pdb=" N ALA A 42 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.705A pdb=" N ALA A 42 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA9, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AB1, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.388A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 601 through 602 removed outlier: 6.717A pdb=" N CYS B 601 " --> pdb=" O GLU F 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 610 through 611 Processing sheet with id=AB4, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.254A pdb=" N GLN O 40 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL O 49 " --> pdb=" O GLN O 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.614A pdb=" N GLN O 101 " --> pdb=" O ASP O 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 18 through 24 Processing sheet with id=AB7, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.254A pdb=" N GLN U 40 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL U 49 " --> pdb=" O GLN U 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.614A pdb=" N GLN U 101 " --> pdb=" O ASP U 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 18 through 24 Processing sheet with id=AC1, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AC2, first strand: chain 'D' and resid 580 through 581 removed outlier: 3.504A pdb=" N ASN C 98 " --> pdb=" O THR D 581 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C 42 " --> pdb=" O HIS C 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 580 through 581 removed outlier: 3.504A pdb=" N ASN C 98 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 610 through 611 Processing sheet with id=AC5, first strand: chain 'F' and resid 544 through 548 Processing sheet with id=AC6, first strand: chain 'F' and resid 580 through 581 removed outlier: 6.841A pdb=" N GLY E 36 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA E 42 " --> pdb=" O HIS E 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 580 through 581 Processing sheet with id=AC8, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC9, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.388A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AD2, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.388A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU E 112 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'P' and resid 60 through 62 removed outlier: 5.168A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'Y' and resid 60 through 62 removed outlier: 5.169A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1122 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: 2.52 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4017 1.35 - 1.47: 3208 1.47 - 1.59: 5228 1.59 - 1.72: 0 1.72 - 1.84: 66 Bond restraints: 12519 Sorted by residual: bond pdb=" CG LEU Y 20 " pdb=" CD1 LEU Y 20 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.57e+00 bond pdb=" CG LEU H 20 " pdb=" CD1 LEU H 20 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.53e+00 bond pdb=" CG LEU P 20 " pdb=" CD1 LEU P 20 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.50e+00 bond pdb=" CG GLN O 37 " pdb=" CD GLN O 37 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.00e+00 bond pdb=" CG GLN L 37 " pdb=" CD GLN L 37 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.94e+00 ... (remaining 12514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 16389 2.33 - 4.66: 522 4.66 - 6.99: 81 6.99 - 9.32: 6 9.32 - 11.65: 9 Bond angle restraints: 17007 Sorted by residual: angle pdb=" N GLY P 101 " pdb=" CA GLY P 101 " pdb=" C GLY P 101 " ideal model delta sigma weight residual 112.34 123.99 -11.65 2.04e+00 2.40e-01 3.26e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 112.34 123.98 -11.64 2.04e+00 2.40e-01 3.26e+01 angle pdb=" N GLY Y 101 " pdb=" CA GLY Y 101 " pdb=" C GLY Y 101 " ideal model delta sigma weight residual 112.34 123.95 -11.61 2.04e+00 2.40e-01 3.24e+01 angle pdb=" N ARG H 100 " pdb=" CA ARG H 100 " pdb=" C ARG H 100 " ideal model delta sigma weight residual 108.52 116.56 -8.04 1.63e+00 3.76e-01 2.43e+01 angle pdb=" N ARG P 100 " pdb=" CA ARG P 100 " pdb=" C ARG P 100 " ideal model delta sigma weight residual 108.52 116.52 -8.00 1.63e+00 3.76e-01 2.41e+01 ... (remaining 17002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 6801 17.35 - 34.70: 505 34.70 - 52.04: 110 52.04 - 69.39: 21 69.39 - 86.74: 18 Dihedral angle restraints: 7455 sinusoidal: 2994 harmonic: 4461 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 147 " pdb=" CB CYS C 147 " ideal model delta sinusoidal sigma weight residual -86.00 0.74 -86.74 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual -86.00 0.73 -86.73 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS E 121 " pdb=" SG CYS E 121 " pdb=" SG CYS E 147 " pdb=" CB CYS E 147 " ideal model delta sinusoidal sigma weight residual -86.00 0.71 -86.71 1 1.00e+01 1.00e-02 9.05e+01 ... (remaining 7452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1798 0.127 - 0.253: 47 0.253 - 0.380: 0 0.380 - 0.507: 0 0.507 - 0.634: 6 Chirality restraints: 1851 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.57e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.55e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.54e+02 ... (remaining 1848 not shown) Planarity restraints: 2217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 235 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" CD GLU A 235 " -0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU A 235 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU A 235 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 235 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" CD GLU C 235 " -0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU C 235 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU C 235 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 235 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" CD GLU E 235 " -0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU E 235 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU E 235 " 0.019 2.00e-02 2.50e+03 ... (remaining 2214 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 756 2.73 - 3.27: 11479 3.27 - 3.81: 18714 3.81 - 4.36: 24579 4.36 - 4.90: 42007 Nonbonded interactions: 97535 Sorted by model distance: nonbonded pdb=" NZ LYS E 114 " pdb=" OD2 ASP Y 56 " model vdw 2.185 3.120 nonbonded pdb=" O GLY Y 101 " pdb=" O HOH Y 301 " model vdw 2.218 3.040 nonbonded pdb=" OE2 GLU H 46 " pdb=" O HOH H 301 " model vdw 2.224 3.040 nonbonded pdb=" O GLY P 101 " pdb=" O HOH P 301 " model vdw 2.229 3.040 nonbonded pdb=" O GLY H 101 " pdb=" O HOH H 302 " model vdw 2.245 3.040 ... (remaining 97530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.210 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 12549 Z= 0.262 Angle : 1.130 26.329 17073 Z= 0.576 Chirality : 0.064 0.634 1851 Planarity : 0.006 0.052 2214 Dihedral : 13.159 85.274 4563 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.28 % Favored : 96.53 % Rotamer: Outliers : 3.27 % Allowed : 5.69 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1554 helix: 0.15 (0.41), residues: 144 sheet: 0.05 (0.21), residues: 555 loop : -0.86 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG C 54 TYR 0.021 0.003 TYR L 94 PHE 0.033 0.003 PHE H 70 TRP 0.015 0.002 TRP Y 114 HIS 0.027 0.005 HIS D 602 Details of bonding type rmsd covalent geometry : bond 0.00594 (12519) covalent geometry : angle 0.99578 (17007) SS BOND : bond 0.01439 ( 24) SS BOND : angle 3.13593 ( 48) hydrogen bonds : bond 0.13735 ( 419) hydrogen bonds : angle 6.78293 ( 1122) link_BETA1-4 : bond 0.06505 ( 3) link_BETA1-4 : angle 22.15334 ( 9) link_NAG-ASN : bond 0.00222 ( 3) link_NAG-ASN : angle 2.53806 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8048 (pttt) cc_final: 0.7800 (pttm) REVERT: L 75 SER cc_start: 0.8085 (OUTLIER) cc_final: 0.7869 (p) REVERT: H 43 LYS cc_start: 0.7623 (mppt) cc_final: 0.7272 (mmtm) REVERT: A 65 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8438 (t) REVERT: A 140 LYS cc_start: 0.8382 (tttt) cc_final: 0.7948 (mtpp) REVERT: A 216 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7834 (m) REVERT: B 567 GLN cc_start: 0.8650 (tt0) cc_final: 0.8367 (tt0) REVERT: B 583 SER cc_start: 0.9027 (p) cc_final: 0.8709 (t) REVERT: B 587 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7423 (ttm110) REVERT: U 48 LYS cc_start: 0.8196 (pttt) cc_final: 0.7976 (pttm) REVERT: D 556 CYS cc_start: 0.7019 (m) cc_final: 0.6673 (m) REVERT: D 587 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7372 (ttm110) REVERT: F 587 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7495 (ttm110) REVERT: C 84 LYS cc_start: 0.8598 (mttt) cc_final: 0.8392 (mtmt) REVERT: C 150 ASP cc_start: 0.7030 (m-30) cc_final: 0.6715 (m-30) REVERT: E 140 LYS cc_start: 0.8446 (tttt) cc_final: 0.8142 (mtpp) REVERT: Y 91 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6561 (pm20) outliers start: 42 outliers final: 6 residues processed: 307 average time/residue: 0.6189 time to fit residues: 205.3970 Evaluate side-chains 212 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain E residue 65 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 ASN L 82 GLN H 31 ASN A 107 ASN A 221 GLN B 516 HIS B 595 GLN O 40 GLN O 82 GLN O 92 GLN U 37 GLN U 55 ASN U 82 GLN D 595 GLN F 516 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 62 GLN C 107 ASN E 62 GLN E 107 ASN P 31 ASN Y 31 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.183403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.148076 restraints weight = 14005.973| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.17 r_work: 0.3381 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12549 Z= 0.130 Angle : 0.675 12.999 17073 Z= 0.349 Chirality : 0.044 0.207 1851 Planarity : 0.005 0.040 2214 Dihedral : 5.504 49.110 1862 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.36 % Allowed : 13.86 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.19), residues: 1554 helix: 1.39 (0.44), residues: 144 sheet: 0.30 (0.20), residues: 576 loop : -0.88 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 54 TYR 0.015 0.001 TYR Y 82 PHE 0.013 0.001 PHE E 225 TRP 0.006 0.001 TRP Y 33 HIS 0.007 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00268 (12519) covalent geometry : angle 0.66551 (17007) SS BOND : bond 0.00437 ( 24) SS BOND : angle 1.66968 ( 48) hydrogen bonds : bond 0.04943 ( 419) hydrogen bonds : angle 5.20357 ( 1122) link_BETA1-4 : bond 0.00355 ( 3) link_BETA1-4 : angle 3.36009 ( 9) link_NAG-ASN : bond 0.00677 ( 3) link_NAG-ASN : angle 1.00464 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 236 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8269 (pttt) cc_final: 0.7988 (pttm) REVERT: L 75 SER cc_start: 0.8534 (p) cc_final: 0.8315 (p) REVERT: H 56 ASP cc_start: 0.8320 (m-30) cc_final: 0.7934 (m-30) REVERT: H 89 ARG cc_start: 0.7451 (ptp-170) cc_final: 0.7210 (ptp90) REVERT: H 91 GLU cc_start: 0.7338 (pm20) cc_final: 0.6960 (pm20) REVERT: A 140 LYS cc_start: 0.8588 (tttt) cc_final: 0.8089 (mtpp) REVERT: A 216 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7524 (p) REVERT: B 587 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7806 (ttm110) REVERT: B 604 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7307 (pp) REVERT: U 48 LYS cc_start: 0.8358 (pttt) cc_final: 0.8118 (pttm) REVERT: D 587 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7597 (ttm110) REVERT: D 600 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7294 (m) REVERT: F 587 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7789 (ttm110) REVERT: C 44 GLN cc_start: 0.6811 (tt0) cc_final: 0.6521 (tt0) REVERT: C 84 LYS cc_start: 0.8846 (mttt) cc_final: 0.8571 (mtmt) REVERT: C 106 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8021 (tp30) REVERT: C 112 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: C 150 ASP cc_start: 0.7369 (m-30) cc_final: 0.7160 (m-30) REVERT: E 112 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: E 140 LYS cc_start: 0.8630 (tttt) cc_final: 0.8264 (mtpp) REVERT: E 216 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8109 (p) REVERT: P 43 LYS cc_start: 0.8177 (mppt) cc_final: 0.7750 (mmtm) REVERT: Y 43 LYS cc_start: 0.7789 (mppt) cc_final: 0.7497 (mmtm) REVERT: Y 54 LYS cc_start: 0.7608 (tppt) cc_final: 0.7332 (tppp) outliers start: 56 outliers final: 26 residues processed: 268 average time/residue: 0.6471 time to fit residues: 187.1612 Evaluate side-chains 242 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 85 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 142 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN B 586 ASN B 595 GLN O 82 GLN D 567 GLN D 595 GLN F 586 ASN F 595 GLN C 39 HIS E 39 HIS E 110 ASN P 31 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.174770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136906 restraints weight = 13718.178| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.17 r_work: 0.3153 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12549 Z= 0.230 Angle : 0.762 12.632 17073 Z= 0.395 Chirality : 0.049 0.164 1851 Planarity : 0.005 0.038 2214 Dihedral : 5.483 37.098 1857 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.76 % Allowed : 14.02 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.19), residues: 1554 helix: 0.84 (0.42), residues: 144 sheet: 0.23 (0.19), residues: 606 loop : -0.96 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 54 TYR 0.015 0.003 TYR H 97 PHE 0.018 0.002 PHE A 225 TRP 0.016 0.002 TRP H 47 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00558 (12519) covalent geometry : angle 0.75073 (17007) SS BOND : bond 0.00797 ( 24) SS BOND : angle 2.09690 ( 48) hydrogen bonds : bond 0.05742 ( 419) hydrogen bonds : angle 4.98995 ( 1122) link_BETA1-4 : bond 0.00268 ( 3) link_BETA1-4 : angle 3.31206 ( 9) link_NAG-ASN : bond 0.00288 ( 3) link_NAG-ASN : angle 1.85487 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 210 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8517 (pttt) cc_final: 0.8203 (pttm) REVERT: L 75 SER cc_start: 0.8662 (p) cc_final: 0.8423 (p) REVERT: H 54 LYS cc_start: 0.7540 (tppt) cc_final: 0.7331 (tptp) REVERT: A 112 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: A 140 LYS cc_start: 0.8785 (tttt) cc_final: 0.8273 (mtpp) REVERT: A 216 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7720 (p) REVERT: B 587 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7772 (ttm110) REVERT: U 48 LYS cc_start: 0.8541 (pttt) cc_final: 0.8284 (pttm) REVERT: D 564 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7539 (mt-10) REVERT: D 587 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7527 (ttm110) REVERT: F 587 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7781 (ttm110) REVERT: C 71 GLU cc_start: 0.7580 (tt0) cc_final: 0.7265 (pt0) REVERT: C 84 LYS cc_start: 0.8966 (mttt) cc_final: 0.8690 (mtpt) REVERT: C 106 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8026 (tp30) REVERT: C 112 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: E 71 GLU cc_start: 0.7580 (tt0) cc_final: 0.7271 (pt0) REVERT: E 112 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: E 140 LYS cc_start: 0.8738 (tttt) cc_final: 0.8309 (mtpp) REVERT: P 43 LYS cc_start: 0.8198 (mppt) cc_final: 0.7886 (mppt) REVERT: P 91 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7011 (pm20) REVERT: Y 43 LYS cc_start: 0.7887 (mppt) cc_final: 0.7622 (mppt) REVERT: Y 89 ARG cc_start: 0.7410 (ptp-170) cc_final: 0.6997 (ptp90) REVERT: Y 91 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7101 (pm20) outliers start: 74 outliers final: 48 residues processed: 255 average time/residue: 0.6492 time to fit residues: 178.3483 Evaluate side-chains 253 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain Y residue 6 GLU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 chunk 155 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN D 595 GLN D 602 HIS F 586 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Y 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.174021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136990 restraints weight = 13579.356| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.08 r_work: 0.3201 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12549 Z= 0.186 Angle : 0.685 12.060 17073 Z= 0.354 Chirality : 0.046 0.154 1851 Planarity : 0.005 0.041 2214 Dihedral : 5.169 33.769 1852 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 6.23 % Allowed : 14.72 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.19), residues: 1554 helix: 0.62 (0.41), residues: 144 sheet: 0.02 (0.20), residues: 567 loop : -0.91 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 54 TYR 0.012 0.002 TYR A 109 PHE 0.016 0.002 PHE P 70 TRP 0.015 0.002 TRP H 47 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00441 (12519) covalent geometry : angle 0.67530 (17007) SS BOND : bond 0.00707 ( 24) SS BOND : angle 1.80068 ( 48) hydrogen bonds : bond 0.05119 ( 419) hydrogen bonds : angle 4.82694 ( 1122) link_BETA1-4 : bond 0.00373 ( 3) link_BETA1-4 : angle 3.01998 ( 9) link_NAG-ASN : bond 0.00224 ( 3) link_NAG-ASN : angle 1.38547 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 200 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8605 (pttt) cc_final: 0.8318 (pttm) REVERT: L 75 SER cc_start: 0.8854 (p) cc_final: 0.8628 (p) REVERT: H 54 LYS cc_start: 0.7603 (tppt) cc_final: 0.7391 (tptp) REVERT: A 112 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: A 140 LYS cc_start: 0.8946 (tttt) cc_final: 0.8449 (mtpp) REVERT: A 216 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7754 (p) REVERT: B 587 ARG cc_start: 0.8400 (mtt180) cc_final: 0.8058 (ttm110) REVERT: B 595 GLN cc_start: 0.7317 (mm-40) cc_final: 0.7113 (mm110) REVERT: O 97 ARG cc_start: 0.8591 (ttp-170) cc_final: 0.8380 (mtm-85) REVERT: U 48 LYS cc_start: 0.8615 (pttt) cc_final: 0.8364 (pttm) REVERT: D 587 ARG cc_start: 0.8364 (mtt180) cc_final: 0.7791 (ttm110) REVERT: D 595 GLN cc_start: 0.7396 (mm-40) cc_final: 0.7129 (mm110) REVERT: F 587 ARG cc_start: 0.8311 (mtt180) cc_final: 0.7367 (mtp85) REVERT: C 71 GLU cc_start: 0.7780 (tt0) cc_final: 0.7509 (pt0) REVERT: C 84 LYS cc_start: 0.9082 (mttt) cc_final: 0.8759 (mtmt) REVERT: C 106 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8235 (tp30) REVERT: C 112 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: E 112 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: E 140 LYS cc_start: 0.8846 (tttt) cc_final: 0.8402 (mtpp) REVERT: P 43 LYS cc_start: 0.8212 (mppt) cc_final: 0.7734 (mppt) REVERT: P 91 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7321 (pm20) REVERT: Y 43 LYS cc_start: 0.7908 (mppt) cc_final: 0.7612 (mppt) REVERT: Y 89 ARG cc_start: 0.7652 (ptp-170) cc_final: 0.7243 (ptp90) REVERT: Y 91 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7315 (pm20) REVERT: Y 92 ASP cc_start: 0.7888 (m-30) cc_final: 0.7622 (m-30) outliers start: 80 outliers final: 52 residues processed: 251 average time/residue: 0.6666 time to fit residues: 180.1823 Evaluate side-chains 249 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain D residue 552 ASP Chi-restraints excluded: chain F residue 552 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain Y residue 6 GLU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 129 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN F 595 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.172053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134243 restraints weight = 13605.099| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.26 r_work: 0.3169 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12549 Z= 0.171 Angle : 0.659 11.894 17073 Z= 0.341 Chirality : 0.046 0.144 1851 Planarity : 0.005 0.041 2214 Dihedral : 5.093 29.382 1852 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.69 % Allowed : 15.65 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 1554 helix: 0.56 (0.41), residues: 144 sheet: -0.01 (0.20), residues: 567 loop : -0.84 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 130 TYR 0.012 0.002 TYR Y 97 PHE 0.014 0.002 PHE C 225 TRP 0.015 0.002 TRP Y 47 HIS 0.010 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00405 (12519) covalent geometry : angle 0.64990 (17007) SS BOND : bond 0.00612 ( 24) SS BOND : angle 1.70226 ( 48) hydrogen bonds : bond 0.04947 ( 419) hydrogen bonds : angle 4.75459 ( 1122) link_BETA1-4 : bond 0.00265 ( 3) link_BETA1-4 : angle 2.94818 ( 9) link_NAG-ASN : bond 0.00178 ( 3) link_NAG-ASN : angle 1.40021 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 195 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8594 (pttt) cc_final: 0.8290 (pttm) REVERT: L 75 SER cc_start: 0.8802 (p) cc_final: 0.8588 (p) REVERT: H 43 LYS cc_start: 0.7718 (mppt) cc_final: 0.7206 (mmtm) REVERT: H 54 LYS cc_start: 0.7620 (tppt) cc_final: 0.7387 (tptp) REVERT: A 112 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: A 140 LYS cc_start: 0.8932 (tttt) cc_final: 0.8460 (mtpp) REVERT: A 216 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7756 (p) REVERT: B 587 ARG cc_start: 0.8359 (mtt180) cc_final: 0.8013 (ttm110) REVERT: U 48 LYS cc_start: 0.8645 (pttt) cc_final: 0.8363 (pttm) REVERT: D 587 ARG cc_start: 0.8342 (mtt180) cc_final: 0.7750 (ttm110) REVERT: D 595 GLN cc_start: 0.7304 (mm-40) cc_final: 0.7088 (mm110) REVERT: F 540 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8217 (mp0) REVERT: F 587 ARG cc_start: 0.8275 (mtt180) cc_final: 0.7337 (mtp85) REVERT: C 71 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: C 84 LYS cc_start: 0.9076 (mttt) cc_final: 0.8737 (mtmt) REVERT: C 106 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8119 (tp30) REVERT: C 112 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: E 106 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7984 (mm-30) REVERT: E 112 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: E 140 LYS cc_start: 0.8841 (tttt) cc_final: 0.8397 (mtpp) REVERT: P 43 LYS cc_start: 0.8178 (mppt) cc_final: 0.7715 (mppt) REVERT: P 91 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7318 (pm20) REVERT: Y 43 LYS cc_start: 0.7882 (mppt) cc_final: 0.7462 (mppt) REVERT: Y 68 ASP cc_start: 0.7620 (m-30) cc_final: 0.7415 (m-30) REVERT: Y 89 ARG cc_start: 0.7771 (ptp-170) cc_final: 0.7443 (ptp90) REVERT: Y 91 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7387 (pm20) REVERT: Y 112 ASP cc_start: 0.8178 (m-30) cc_final: 0.7929 (m-30) outliers start: 73 outliers final: 48 residues processed: 241 average time/residue: 0.6327 time to fit residues: 164.6737 Evaluate side-chains 243 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 105 CYS Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 GLN F 586 ASN F 595 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.171290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133540 restraints weight = 13661.661| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.17 r_work: 0.3163 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12549 Z= 0.185 Angle : 0.673 11.441 17073 Z= 0.348 Chirality : 0.046 0.137 1851 Planarity : 0.005 0.043 2214 Dihedral : 5.115 27.285 1852 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.45 % Allowed : 15.50 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1554 helix: 0.47 (0.40), residues: 144 sheet: -0.05 (0.20), residues: 567 loop : -0.84 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 130 TYR 0.013 0.002 TYR Y 97 PHE 0.015 0.002 PHE A 225 TRP 0.016 0.002 TRP Y 47 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00442 (12519) covalent geometry : angle 0.65979 (17007) SS BOND : bond 0.00729 ( 24) SS BOND : angle 2.22677 ( 48) hydrogen bonds : bond 0.05088 ( 419) hydrogen bonds : angle 4.71286 ( 1122) link_BETA1-4 : bond 0.00263 ( 3) link_BETA1-4 : angle 2.96832 ( 9) link_NAG-ASN : bond 0.00143 ( 3) link_NAG-ASN : angle 1.48467 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 192 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8504 (pttt) cc_final: 0.8280 (pttp) REVERT: L 75 SER cc_start: 0.8636 (p) cc_final: 0.8408 (p) REVERT: A 112 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: A 140 LYS cc_start: 0.8803 (tttt) cc_final: 0.8354 (mtpp) REVERT: A 216 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7756 (p) REVERT: B 587 ARG cc_start: 0.8104 (mtt180) cc_final: 0.7763 (ttm110) REVERT: U 48 LYS cc_start: 0.8553 (pttt) cc_final: 0.8265 (pttm) REVERT: U 57 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8699 (mtm180) REVERT: D 587 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7494 (ttm110) REVERT: F 587 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7178 (mtp85) REVERT: C 84 LYS cc_start: 0.8994 (mttt) cc_final: 0.8683 (mtmt) REVERT: C 112 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: C 156 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8132 (mm-30) REVERT: E 112 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: E 140 LYS cc_start: 0.8727 (tttt) cc_final: 0.8284 (mtpp) REVERT: P 43 LYS cc_start: 0.8106 (mppt) cc_final: 0.7789 (mppt) REVERT: P 91 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7486 (pm20) REVERT: P 112 ASP cc_start: 0.8511 (m-30) cc_final: 0.8270 (m-30) REVERT: Y 89 ARG cc_start: 0.7834 (ptp-170) cc_final: 0.7508 (ptp90) REVERT: Y 91 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7312 (pm20) REVERT: Y 112 ASP cc_start: 0.8065 (m-30) cc_final: 0.7838 (m-30) outliers start: 70 outliers final: 49 residues processed: 236 average time/residue: 0.6254 time to fit residues: 159.6045 Evaluate side-chains 237 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 182 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 105 CYS Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 107 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN F 586 ASN F 595 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.172568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.134885 restraints weight = 13607.244| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.14 r_work: 0.3195 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12549 Z= 0.146 Angle : 0.628 11.365 17073 Z= 0.324 Chirality : 0.044 0.144 1851 Planarity : 0.004 0.041 2214 Dihedral : 4.977 26.689 1852 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.06 % Allowed : 16.28 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1554 helix: 0.61 (0.41), residues: 144 sheet: -0.06 (0.20), residues: 567 loop : -0.75 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 130 TYR 0.011 0.002 TYR H 97 PHE 0.013 0.001 PHE F 582 TRP 0.013 0.001 TRP Y 47 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00338 (12519) covalent geometry : angle 0.61585 (17007) SS BOND : bond 0.00612 ( 24) SS BOND : angle 2.01026 ( 48) hydrogen bonds : bond 0.04646 ( 419) hydrogen bonds : angle 4.65096 ( 1122) link_BETA1-4 : bond 0.00324 ( 3) link_BETA1-4 : angle 2.84852 ( 9) link_NAG-ASN : bond 0.00274 ( 3) link_NAG-ASN : angle 1.32621 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 192 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 SER cc_start: 0.8629 (p) cc_final: 0.8413 (p) REVERT: A 71 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: A 112 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: A 140 LYS cc_start: 0.8788 (tttt) cc_final: 0.8332 (mtpp) REVERT: B 587 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7774 (ttm110) REVERT: U 57 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8700 (mtm180) REVERT: D 587 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7499 (ttm110) REVERT: F 587 ARG cc_start: 0.8031 (mtt180) cc_final: 0.7188 (mtp85) REVERT: C 84 LYS cc_start: 0.8999 (mttt) cc_final: 0.8710 (mtmt) REVERT: C 112 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: C 156 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: E 112 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: E 140 LYS cc_start: 0.8741 (tttt) cc_final: 0.8301 (mtpp) REVERT: Y 89 ARG cc_start: 0.7823 (ptp-170) cc_final: 0.7532 (ptp90) REVERT: Y 91 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7183 (pm20) REVERT: Y 112 ASP cc_start: 0.8024 (m-30) cc_final: 0.7801 (m-30) outliers start: 65 outliers final: 48 residues processed: 230 average time/residue: 0.6497 time to fit residues: 160.9505 Evaluate side-chains 241 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 105 CYS Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 GLN D 595 GLN F 586 ASN F 595 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.172075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134301 restraints weight = 13548.720| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.07 r_work: 0.3193 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12549 Z= 0.156 Angle : 0.639 11.220 17073 Z= 0.330 Chirality : 0.045 0.139 1851 Planarity : 0.005 0.052 2214 Dihedral : 4.948 26.486 1851 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.91 % Allowed : 17.83 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.20), residues: 1554 helix: 0.57 (0.40), residues: 144 sheet: -0.07 (0.20), residues: 567 loop : -0.71 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 596 TYR 0.012 0.002 TYR F 517 PHE 0.013 0.002 PHE A 225 TRP 0.013 0.002 TRP Y 47 HIS 0.003 0.001 HIS E 154 Details of bonding type rmsd covalent geometry : bond 0.00365 (12519) covalent geometry : angle 0.62729 (17007) SS BOND : bond 0.00606 ( 24) SS BOND : angle 2.00106 ( 48) hydrogen bonds : bond 0.04673 ( 419) hydrogen bonds : angle 4.57743 ( 1122) link_BETA1-4 : bond 0.00277 ( 3) link_BETA1-4 : angle 2.82921 ( 9) link_NAG-ASN : bond 0.00211 ( 3) link_NAG-ASN : angle 1.34085 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 75 SER cc_start: 0.8630 (p) cc_final: 0.8429 (p) REVERT: L 88 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7454 (t0) REVERT: A 112 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: A 140 LYS cc_start: 0.8800 (tttt) cc_final: 0.8344 (mtpp) REVERT: B 587 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7771 (ttm110) REVERT: U 57 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8709 (mtm180) REVERT: D 587 ARG cc_start: 0.8098 (mtt180) cc_final: 0.7498 (ttm110) REVERT: F 587 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7190 (mtp85) REVERT: C 84 LYS cc_start: 0.9004 (mttt) cc_final: 0.8710 (mtmt) REVERT: C 112 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: C 156 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: E 112 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: E 140 LYS cc_start: 0.8750 (tttt) cc_final: 0.8308 (mtpp) REVERT: P 91 GLU cc_start: 0.7717 (pm20) cc_final: 0.7348 (pm20) REVERT: P 112 ASP cc_start: 0.8522 (m-30) cc_final: 0.8308 (m-30) REVERT: Y 56 ASP cc_start: 0.8467 (m-30) cc_final: 0.8200 (m-30) REVERT: Y 112 ASP cc_start: 0.8002 (m-30) cc_final: 0.7799 (m-30) outliers start: 63 outliers final: 48 residues processed: 220 average time/residue: 0.6955 time to fit residues: 164.6297 Evaluate side-chains 238 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 184 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 105 CYS Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 144 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN F 586 ASN F 595 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.169990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132008 restraints weight = 13592.562| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.21 r_work: 0.3154 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12549 Z= 0.216 Angle : 0.704 11.149 17073 Z= 0.364 Chirality : 0.047 0.150 1851 Planarity : 0.005 0.055 2214 Dihedral : 5.166 27.543 1851 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.83 % Allowed : 17.91 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.20), residues: 1554 helix: 0.39 (0.40), residues: 144 sheet: -0.13 (0.20), residues: 567 loop : -0.86 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 596 TYR 0.015 0.002 TYR Y 97 PHE 0.015 0.002 PHE E 225 TRP 0.017 0.002 TRP Y 47 HIS 0.003 0.001 HIS E 154 Details of bonding type rmsd covalent geometry : bond 0.00520 (12519) covalent geometry : angle 0.69044 (17007) SS BOND : bond 0.00771 ( 24) SS BOND : angle 2.26928 ( 48) hydrogen bonds : bond 0.05396 ( 419) hydrogen bonds : angle 4.68724 ( 1122) link_BETA1-4 : bond 0.00083 ( 3) link_BETA1-4 : angle 3.12065 ( 9) link_NAG-ASN : bond 0.00073 ( 3) link_NAG-ASN : angle 1.60064 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 182 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: H 89 ARG cc_start: 0.7835 (ptp90) cc_final: 0.7229 (ptp90) REVERT: A 112 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: A 140 LYS cc_start: 0.8963 (tttt) cc_final: 0.8507 (mtpp) REVERT: B 587 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7992 (ttm110) REVERT: D 587 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7741 (ttm110) REVERT: F 587 ARG cc_start: 0.8294 (mtt180) cc_final: 0.7655 (ttm110) REVERT: C 84 LYS cc_start: 0.9092 (mttt) cc_final: 0.8744 (mtmt) REVERT: C 112 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: C 140 LYS cc_start: 0.8959 (tttt) cc_final: 0.8505 (mtpp) REVERT: E 112 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: E 140 LYS cc_start: 0.8893 (tttt) cc_final: 0.8438 (mtpp) REVERT: P 43 LYS cc_start: 0.7955 (mppt) cc_final: 0.7733 (mppt) REVERT: P 91 GLU cc_start: 0.8037 (pm20) cc_final: 0.7539 (pm20) REVERT: P 112 ASP cc_start: 0.8674 (m-30) cc_final: 0.8452 (m-30) REVERT: Y 48 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7917 (p) outliers start: 62 outliers final: 51 residues processed: 218 average time/residue: 0.6808 time to fit residues: 159.8496 Evaluate side-chains 235 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 6 GLU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 105 CYS Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 40.0000 chunk 25 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN F 586 ASN F 595 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.171294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133675 restraints weight = 13587.504| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.09 r_work: 0.3165 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12549 Z= 0.172 Angle : 0.655 11.084 17073 Z= 0.339 Chirality : 0.045 0.166 1851 Planarity : 0.005 0.045 2214 Dihedral : 5.032 27.279 1851 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.28 % Allowed : 18.77 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1554 helix: 0.49 (0.40), residues: 144 sheet: -0.10 (0.20), residues: 567 loop : -0.82 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Y 89 TYR 0.013 0.002 TYR F 517 PHE 0.013 0.002 PHE F 582 TRP 0.015 0.002 TRP Y 47 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00409 (12519) covalent geometry : angle 0.64305 (17007) SS BOND : bond 0.00624 ( 24) SS BOND : angle 2.01026 ( 48) hydrogen bonds : bond 0.04841 ( 419) hydrogen bonds : angle 4.62523 ( 1122) link_BETA1-4 : bond 0.00302 ( 3) link_BETA1-4 : angle 2.89573 ( 9) link_NAG-ASN : bond 0.00283 ( 3) link_NAG-ASN : angle 1.38218 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: H 89 ARG cc_start: 0.7831 (ptp90) cc_final: 0.7265 (ptp90) REVERT: A 71 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7140 (pt0) REVERT: A 84 LYS cc_start: 0.9077 (mttt) cc_final: 0.8729 (mtpt) REVERT: A 112 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: A 140 LYS cc_start: 0.8793 (tttt) cc_final: 0.8343 (mtpp) REVERT: B 587 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7731 (ttm110) REVERT: D 587 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7475 (ttm110) REVERT: F 587 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7194 (mtp85) REVERT: C 84 LYS cc_start: 0.9008 (mttt) cc_final: 0.8695 (mtmt) REVERT: C 112 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: E 112 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: E 140 LYS cc_start: 0.8739 (tttt) cc_final: 0.8290 (mtpp) REVERT: P 43 LYS cc_start: 0.8008 (mppt) cc_final: 0.7770 (mppt) REVERT: P 56 ASP cc_start: 0.8476 (m-30) cc_final: 0.8212 (m-30) REVERT: P 91 GLU cc_start: 0.7886 (pm20) cc_final: 0.7550 (pm20) REVERT: P 112 ASP cc_start: 0.8537 (m-30) cc_final: 0.8315 (m-30) REVERT: Y 43 LYS cc_start: 0.7803 (mppt) cc_final: 0.7555 (mppt) REVERT: Y 56 ASP cc_start: 0.8507 (m-30) cc_final: 0.8229 (m-30) outliers start: 55 outliers final: 48 residues processed: 217 average time/residue: 0.6784 time to fit residues: 158.5339 Evaluate side-chains 235 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain D residue 601 CYS Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 61 ASP Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 105 CYS Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 96 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN D 595 GLN F 586 ASN F 595 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.172567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.134845 restraints weight = 13550.812| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.10 r_work: 0.3184 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12549 Z= 0.117 Angle : 0.593 11.114 17073 Z= 0.305 Chirality : 0.043 0.177 1851 Planarity : 0.004 0.038 2214 Dihedral : 4.788 25.992 1851 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.27 % Allowed : 20.02 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1554 helix: 0.79 (0.41), residues: 144 sheet: -0.02 (0.20), residues: 567 loop : -0.71 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 89 TYR 0.013 0.001 TYR F 517 PHE 0.011 0.001 PHE F 582 TRP 0.009 0.001 TRP P 47 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00264 (12519) covalent geometry : angle 0.58387 (17007) SS BOND : bond 0.00462 ( 24) SS BOND : angle 1.70469 ( 48) hydrogen bonds : bond 0.04030 ( 419) hydrogen bonds : angle 4.51042 ( 1122) link_BETA1-4 : bond 0.00385 ( 3) link_BETA1-4 : angle 2.60116 ( 9) link_NAG-ASN : bond 0.00460 ( 3) link_NAG-ASN : angle 1.14568 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4465.38 seconds wall clock time: 76 minutes 48.10 seconds (4608.10 seconds total)