Starting phenix.real_space_refine on Wed Jul 30 09:55:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s8j_10124/07_2025/6s8j_10124.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8j_10124/07_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_10124/07_2025/6s8j_10124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8j_10124/07_2025/6s8j_10124.map" model { file = "/net/cci-nas-00/data/ceres_data/6s8j_10124/07_2025/6s8j_10124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8j_10124/07_2025/6s8j_10124.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, D, F, I, J, C, E Time building chain proxies: 6.27, per 1000 atoms: 0.51 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: 2.76 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.97 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: 4.33 Time building geometry restraints manager: 3.35 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: 0.08 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 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.860 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 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:15.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (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 TRP 0.015 0.002 TRP Y 114 HIS 0.027 0.005 HIS D 602 PHE 0.033 0.003 PHE H 70 TYR 0.021 0.003 TYR L 94 ARG 0.028 0.002 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 3) link_NAG-ASN : angle 2.53806 ( 9) link_BETA1-4 : bond 0.06505 ( 3) link_BETA1-4 : angle 22.15334 ( 9) hydrogen bonds : bond 0.13735 ( 419) hydrogen bonds : angle 6.78293 ( 1122) SS BOND : bond 0.01439 ( 24) SS BOND : angle 3.13593 ( 48) covalent geometry : bond 0.00594 (12519) covalent geometry : angle 0.99578 (17007) *********************** 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 : 1.668 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: 1.3017 time to fit residues: 433.4047 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 : 1.456 ------------------------------------------------------------------------------- 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 131 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.180123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.143444 restraints weight = 13970.095| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.27 r_work: 0.3331 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12549 Z= 0.150 Angle : 0.704 13.685 17073 Z= 0.365 Chirality : 0.045 0.181 1851 Planarity : 0.005 0.042 2214 Dihedral : 5.599 49.472 1862 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.75 % Allowed : 13.94 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 1554 helix: 1.30 (0.44), residues: 144 sheet: 0.29 (0.20), residues: 576 loop : -0.91 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.006 0.001 HIS A 39 PHE 0.016 0.001 PHE E 225 TYR 0.014 0.002 TYR Y 82 ARG 0.006 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 3) link_NAG-ASN : angle 1.11056 ( 9) link_BETA1-4 : bond 0.00281 ( 3) link_BETA1-4 : angle 3.57841 ( 9) hydrogen bonds : bond 0.05272 ( 419) hydrogen bonds : angle 5.17913 ( 1122) SS BOND : bond 0.00461 ( 24) SS BOND : angle 1.81398 ( 48) covalent geometry : bond 0.00329 (12519) covalent geometry : angle 0.69307 (17007) *********************** 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: 61 poor density : 231 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8383 (pttt) cc_final: 0.8073 (pttm) REVERT: L 75 SER cc_start: 0.8581 (p) cc_final: 0.8349 (p) REVERT: H 56 ASP cc_start: 0.8378 (m-30) cc_final: 0.7939 (m-30) REVERT: H 89 ARG cc_start: 0.7461 (ptp-170) cc_final: 0.7192 (ptp90) REVERT: H 91 GLU cc_start: 0.7367 (pm20) cc_final: 0.6953 (pm20) REVERT: A 140 LYS cc_start: 0.8631 (tttt) cc_final: 0.8131 (mtpp) REVERT: B 587 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7791 (ttm110) REVERT: B 604 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7324 (pp) REVERT: U 48 LYS cc_start: 0.8441 (pttt) cc_final: 0.8179 (pttm) REVERT: D 587 ARG cc_start: 0.8096 (mtt180) cc_final: 0.7591 (ttm110) REVERT: D 600 THR cc_start: 0.7509 (OUTLIER) cc_final: 0.7302 (m) REVERT: F 587 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7752 (ttm110) REVERT: C 44 GLN cc_start: 0.6840 (tt0) cc_final: 0.6515 (tt0) REVERT: C 84 LYS cc_start: 0.8892 (mttt) cc_final: 0.8593 (mtpt) REVERT: C 106 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8041 (tp30) REVERT: C 112 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: C 150 ASP cc_start: 0.7576 (m-30) cc_final: 0.7317 (m-30) REVERT: C 156 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8353 (mm-30) REVERT: C 216 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8225 (p) REVERT: E 112 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: E 140 LYS cc_start: 0.8652 (tttt) cc_final: 0.8304 (mtpp) REVERT: P 43 LYS cc_start: 0.8152 (mppt) cc_final: 0.7708 (mmtm) REVERT: Y 43 LYS cc_start: 0.7800 (mppt) cc_final: 0.7469 (mmtm) outliers start: 61 outliers final: 31 residues processed: 267 average time/residue: 1.3659 time to fit residues: 394.6365 Evaluate side-chains 250 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 21 SER 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 88 ASP 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 567 GLN 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 156 GLU 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 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 7 SER 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 96 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 595 GLN F 595 GLN C 39 HIS C 44 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.176683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139208 restraints weight = 13661.952| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.11 r_work: 0.3199 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12549 Z= 0.183 Angle : 0.706 12.907 17073 Z= 0.364 Chirality : 0.047 0.146 1851 Planarity : 0.005 0.036 2214 Dihedral : 5.356 37.069 1857 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 5.69 % Allowed : 14.56 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.19), residues: 1554 helix: 0.98 (0.43), residues: 144 sheet: 0.28 (0.19), residues: 585 loop : -0.95 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.003 0.001 HIS A 154 PHE 0.016 0.002 PHE A 225 TYR 0.013 0.002 TYR H 97 ARG 0.005 0.001 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 3) link_NAG-ASN : angle 1.63270 ( 9) link_BETA1-4 : bond 0.00340 ( 3) link_BETA1-4 : angle 3.17231 ( 9) hydrogen bonds : bond 0.05245 ( 419) hydrogen bonds : angle 4.94202 ( 1122) SS BOND : bond 0.00642 ( 24) SS BOND : angle 1.85756 ( 48) covalent geometry : bond 0.00434 (12519) covalent geometry : angle 0.69546 (17007) *********************** 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 286 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 213 time to evaluate : 1.540 Fit side-chains revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8484 (pttt) cc_final: 0.8171 (pttm) REVERT: L 75 SER cc_start: 0.8643 (p) cc_final: 0.8417 (p) REVERT: A 45 VAL cc_start: 0.7237 (OUTLIER) cc_final: 0.6887 (t) REVERT: A 112 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: A 140 LYS cc_start: 0.8756 (tttt) cc_final: 0.8247 (mtpp) REVERT: A 216 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7701 (p) REVERT: B 587 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7779 (ttm110) REVERT: U 48 LYS cc_start: 0.8523 (pttt) cc_final: 0.8266 (pttm) REVERT: U 57 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8555 (mtm180) REVERT: D 587 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7529 (ttm110) REVERT: F 587 ARG cc_start: 0.8061 (mtt180) cc_final: 0.7597 (ttm110) REVERT: C 44 GLN cc_start: 0.6742 (tt0) cc_final: 0.6413 (tt0) REVERT: C 71 GLU cc_start: 0.7561 (tt0) cc_final: 0.7307 (pt0) REVERT: C 84 LYS cc_start: 0.8939 (mttt) cc_final: 0.8675 (mtpt) REVERT: C 112 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: C 156 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8424 (mm-30) REVERT: E 71 GLU cc_start: 0.7575 (tt0) cc_final: 0.7277 (pt0) REVERT: E 112 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: E 140 LYS cc_start: 0.8711 (tttt) cc_final: 0.8293 (mtpp) REVERT: P 43 LYS cc_start: 0.8149 (mppt) cc_final: 0.7847 (mppt) REVERT: P 91 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6945 (pm20) REVERT: Y 43 LYS cc_start: 0.7850 (mppt) cc_final: 0.7605 (mppt) REVERT: Y 54 LYS cc_start: 0.7644 (tppt) cc_final: 0.7364 (tppp) REVERT: Y 91 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7108 (pm20) outliers start: 73 outliers final: 43 residues processed: 260 average time/residue: 1.8515 time to fit residues: 520.1180 Evaluate side-chains 256 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 112 GLU 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 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 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 156 GLU 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 6 GLU 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 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 21 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 66 VAL 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 102 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 145 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.171810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134016 restraints weight = 13576.552| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.18 r_work: 0.3174 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12549 Z= 0.196 Angle : 0.699 12.093 17073 Z= 0.361 Chirality : 0.047 0.146 1851 Planarity : 0.005 0.041 2214 Dihedral : 5.189 34.082 1852 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.69 % Allowed : 15.03 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1554 helix: 0.69 (0.41), residues: 144 sheet: 0.09 (0.20), residues: 561 loop : -0.92 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.005 0.001 HIS C 39 PHE 0.016 0.002 PHE P 70 TYR 0.013 0.002 TYR A 109 ARG 0.007 0.001 ARG E 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 3) link_NAG-ASN : angle 1.48498 ( 9) link_BETA1-4 : bond 0.00201 ( 3) link_BETA1-4 : angle 3.13975 ( 9) hydrogen bonds : bond 0.05283 ( 419) hydrogen bonds : angle 4.83273 ( 1122) SS BOND : bond 0.00695 ( 24) SS BOND : angle 1.91054 ( 48) covalent geometry : bond 0.00468 (12519) covalent geometry : angle 0.68852 (17007) *********************** 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: 73 poor density : 207 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8619 (pttt) cc_final: 0.8330 (pttm) REVERT: L 75 SER cc_start: 0.8844 (p) cc_final: 0.8621 (p) REVERT: H 43 LYS cc_start: 0.7920 (mppt) cc_final: 0.7302 (mmtm) REVERT: A 112 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: A 140 LYS cc_start: 0.8941 (tttt) cc_final: 0.8443 (mtpp) REVERT: A 216 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7726 (p) REVERT: B 587 ARG cc_start: 0.8407 (mtt180) cc_final: 0.8033 (ttm110) REVERT: B 595 GLN cc_start: 0.7326 (mm-40) cc_final: 0.7111 (mm110) REVERT: U 48 LYS cc_start: 0.8632 (pttt) cc_final: 0.8369 (pttm) REVERT: D 587 ARG cc_start: 0.8370 (mtt180) cc_final: 0.7772 (ttm110) REVERT: D 595 GLN cc_start: 0.7342 (mm-40) cc_final: 0.7079 (mm110) REVERT: F 587 ARG cc_start: 0.8303 (mtt180) cc_final: 0.7827 (ttm110) REVERT: C 71 GLU cc_start: 0.7783 (tt0) cc_final: 0.7517 (pt0) REVERT: C 84 LYS cc_start: 0.9064 (mttt) cc_final: 0.8733 (mtmt) REVERT: C 112 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: C 140 LYS cc_start: 0.8937 (tttt) cc_final: 0.8486 (mtpp) REVERT: C 156 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8623 (mm-30) REVERT: E 112 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: E 140 LYS cc_start: 0.8850 (tttt) cc_final: 0.8408 (mtpp) REVERT: P 43 LYS cc_start: 0.8205 (mppt) cc_final: 0.7724 (mppt) REVERT: P 89 ARG cc_start: 0.7761 (ptp90) cc_final: 0.7408 (ptp90) REVERT: P 91 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7296 (pm20) REVERT: Y 43 LYS cc_start: 0.7898 (mppt) cc_final: 0.7612 (mppt) REVERT: Y 89 ARG cc_start: 0.7729 (ptp-170) cc_final: 0.7443 (ptp90) REVERT: Y 91 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7295 (pm20) outliers start: 73 outliers final: 49 residues processed: 251 average time/residue: 1.6215 time to fit residues: 439.7729 Evaluate side-chains 250 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 196 time to evaluate : 2.785 ------------------------------------------------------------------------------- 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 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 112 GLU 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 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 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 90 SER 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 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 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 21 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 66 VAL 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 126 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 143 optimal weight: 0.0370 chunk 89 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 overall best weight: 1.7462 ------------------------------------------------------------------------------- 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 567 GLN F 595 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Y 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.174057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136928 restraints weight = 13507.769| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.03 r_work: 0.3222 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12549 Z= 0.159 Angle : 0.643 12.015 17073 Z= 0.333 Chirality : 0.045 0.139 1851 Planarity : 0.005 0.040 2214 Dihedral : 5.035 28.358 1852 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.30 % Allowed : 15.89 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.19), residues: 1554 helix: 0.70 (0.41), residues: 144 sheet: 0.09 (0.20), residues: 561 loop : -0.83 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 47 HIS 0.003 0.001 HIS A 154 PHE 0.013 0.002 PHE A 225 TYR 0.011 0.002 TYR H 97 ARG 0.006 0.001 ARG C 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 3) link_NAG-ASN : angle 1.30364 ( 9) link_BETA1-4 : bond 0.00286 ( 3) link_BETA1-4 : angle 2.91071 ( 9) hydrogen bonds : bond 0.04769 ( 419) hydrogen bonds : angle 4.73030 ( 1122) SS BOND : bond 0.00555 ( 24) SS BOND : angle 1.60837 ( 48) covalent geometry : bond 0.00374 (12519) covalent geometry : angle 0.63463 (17007) *********************** 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 263 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 195 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8495 (pttt) cc_final: 0.8205 (pttm) REVERT: L 75 SER cc_start: 0.8660 (p) cc_final: 0.8434 (p) REVERT: A 112 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: A 140 LYS cc_start: 0.8783 (tttt) cc_final: 0.8316 (mtpp) REVERT: A 216 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7775 (p) REVERT: B 587 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7786 (ttm110) REVERT: U 48 LYS cc_start: 0.8550 (pttt) cc_final: 0.8280 (pttm) REVERT: D 587 ARG cc_start: 0.8139 (mtt180) cc_final: 0.7555 (ttm110) REVERT: F 587 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7589 (ttm110) REVERT: C 84 LYS cc_start: 0.8976 (mttt) cc_final: 0.8696 (mtmt) REVERT: C 112 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: C 156 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8436 (mm-30) REVERT: E 106 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7811 (mm-30) REVERT: E 112 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: E 140 LYS cc_start: 0.8727 (tttt) cc_final: 0.8315 (mtpp) REVERT: P 43 LYS cc_start: 0.8164 (mppt) cc_final: 0.7727 (mppt) REVERT: P 56 ASP cc_start: 0.8583 (m-30) cc_final: 0.8282 (m-30) REVERT: P 91 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7139 (pm20) REVERT: Y 43 LYS cc_start: 0.7833 (mppt) cc_final: 0.7454 (mppt) REVERT: Y 89 ARG cc_start: 0.7832 (ptp-170) cc_final: 0.7411 (ptp90) REVERT: Y 91 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7203 (pm20) REVERT: Y 112 ASP cc_start: 0.8036 (m-30) cc_final: 0.7764 (m-30) outliers start: 68 outliers final: 39 residues processed: 239 average time/residue: 1.5731 time to fit residues: 410.6731 Evaluate side-chains 233 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 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 106 GLU Chi-restraints excluded: chain A residue 112 GLU 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 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 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 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 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 59 THR 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 66 VAL 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 33 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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** B 595 GLN D 595 GLN F 595 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** 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 = 0.3872 r_free = 0.3872 target = 0.169135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131288 restraints weight = 13797.449| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.27 r_work: 0.3179 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12549 Z= 0.206 Angle : 0.701 11.327 17073 Z= 0.362 Chirality : 0.047 0.139 1851 Planarity : 0.005 0.043 2214 Dihedral : 5.191 27.541 1852 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.22 % Allowed : 16.36 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.19), residues: 1554 helix: 0.54 (0.41), residues: 144 sheet: 0.04 (0.20), residues: 561 loop : -0.84 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Y 47 HIS 0.003 0.001 HIS E 154 PHE 0.016 0.002 PHE E 225 TYR 0.013 0.002 TYR Y 97 ARG 0.006 0.001 ARG A 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 3) link_NAG-ASN : angle 1.58800 ( 9) link_BETA1-4 : bond 0.00066 ( 3) link_BETA1-4 : angle 3.13649 ( 9) hydrogen bonds : bond 0.05348 ( 419) hydrogen bonds : angle 4.75970 ( 1122) SS BOND : bond 0.00825 ( 24) SS BOND : angle 2.38257 ( 48) covalent geometry : bond 0.00495 (12519) covalent geometry : angle 0.68583 (17007) *********************** 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 256 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 189 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 SER cc_start: 0.8810 (p) cc_final: 0.8609 (p) REVERT: A 112 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: A 140 LYS cc_start: 0.8950 (tttt) cc_final: 0.8494 (mtpp) REVERT: A 216 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7762 (p) REVERT: B 587 ARG cc_start: 0.8405 (mtt180) cc_final: 0.8048 (ttm110) REVERT: B 595 GLN cc_start: 0.7369 (mm-40) cc_final: 0.7125 (mm110) REVERT: U 48 LYS cc_start: 0.8630 (pttt) cc_final: 0.8354 (pttm) REVERT: D 587 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7771 (ttm110) REVERT: D 595 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7117 (mm110) REVERT: F 587 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7347 (ttt90) REVERT: C 84 LYS cc_start: 0.9070 (mttt) cc_final: 0.8734 (mtmt) REVERT: C 112 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: C 140 LYS cc_start: 0.8938 (tttt) cc_final: 0.8497 (mtpp) REVERT: E 112 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: E 140 LYS cc_start: 0.8864 (tttt) cc_final: 0.8422 (mtpp) REVERT: E 156 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8202 (mm-30) REVERT: P 43 LYS cc_start: 0.8144 (mppt) cc_final: 0.7809 (mppt) REVERT: P 56 ASP cc_start: 0.8642 (m-30) cc_final: 0.8368 (m-30) REVERT: P 91 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7635 (pm20) REVERT: Y 48 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7912 (p) REVERT: Y 89 ARG cc_start: 0.7897 (ptp-170) cc_final: 0.7529 (ptp90) REVERT: Y 91 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7366 (pm20) outliers start: 67 outliers final: 46 residues processed: 228 average time/residue: 1.3421 time to fit residues: 331.1239 Evaluate side-chains 232 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 106 GLU Chi-restraints excluded: chain A residue 112 GLU 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 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 90 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 156 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 25 SER Chi-restraints excluded: chain P residue 51 ILE 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 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 51 ILE Chi-restraints excluded: chain Y residue 66 VAL 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 114 optimal weight: 6.9990 chunk 149 optimal weight: 0.0370 chunk 148 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 0.0470 chunk 129 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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** A 62 GLN U 37 GLN F 595 GLN C 44 GLN C 188 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.174718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137011 restraints weight = 13673.750| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.15 r_work: 0.3244 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12549 Z= 0.109 Angle : 0.583 11.385 17073 Z= 0.300 Chirality : 0.043 0.151 1851 Planarity : 0.004 0.036 2214 Dihedral : 4.801 25.905 1852 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.74 % Allowed : 18.07 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1554 helix: 0.84 (0.41), residues: 144 sheet: 0.10 (0.20), residues: 561 loop : -0.66 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 47 HIS 0.002 0.001 HIS C 154 PHE 0.010 0.001 PHE F 582 TYR 0.011 0.001 TYR E 137 ARG 0.007 0.000 ARG C 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 3) link_NAG-ASN : angle 1.06050 ( 9) link_BETA1-4 : bond 0.00558 ( 3) link_BETA1-4 : angle 2.57647 ( 9) hydrogen bonds : bond 0.04037 ( 419) hydrogen bonds : angle 4.62936 ( 1122) SS BOND : bond 0.00422 ( 24) SS BOND : angle 1.78632 ( 48) covalent geometry : bond 0.00237 (12519) covalent geometry : angle 0.57270 (17007) *********************** 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 243 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: A 140 LYS cc_start: 0.8750 (tttt) cc_final: 0.8293 (mtpp) REVERT: B 587 ARG cc_start: 0.8104 (mtt180) cc_final: 0.7770 (ttm110) REVERT: D 587 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7524 (ttm110) REVERT: F 587 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7615 (ttm110) REVERT: C 84 LYS cc_start: 0.8971 (mttt) cc_final: 0.8705 (mtmt) REVERT: C 112 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: E 140 LYS cc_start: 0.8729 (tttt) cc_final: 0.8319 (mtpp) REVERT: P 43 LYS cc_start: 0.8053 (mppt) cc_final: 0.7692 (mppt) REVERT: P 56 ASP cc_start: 0.8574 (m-30) cc_final: 0.8340 (m-30) REVERT: P 112 ASP cc_start: 0.8477 (m-30) cc_final: 0.8274 (m-30) REVERT: Y 43 LYS cc_start: 0.7764 (mppt) cc_final: 0.7486 (mppt) REVERT: Y 56 ASP cc_start: 0.8489 (m-30) cc_final: 0.8160 (m-30) REVERT: Y 91 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7245 (pm20) outliers start: 48 outliers final: 32 residues processed: 221 average time/residue: 1.5750 time to fit residues: 375.5522 Evaluate side-chains 221 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 112 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain O residue 22 SER 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 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 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 66 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 61 ASP Chi-restraints excluded: chain Y residue 66 VAL 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 65 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** B 595 GLN U 37 GLN D 567 GLN D 595 GLN F 595 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.169345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131199 restraints weight = 13782.983| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.37 r_work: 0.3180 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12549 Z= 0.197 Angle : 0.681 11.190 17073 Z= 0.351 Chirality : 0.046 0.148 1851 Planarity : 0.005 0.045 2214 Dihedral : 5.046 26.869 1851 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.05 % Allowed : 18.61 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.20), residues: 1554 helix: 1.29 (0.42), residues: 126 sheet: -0.07 (0.20), residues: 567 loop : -0.73 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 47 HIS 0.003 0.001 HIS E 154 PHE 0.015 0.002 PHE A 225 TYR 0.014 0.002 TYR Y 97 ARG 0.010 0.001 ARG B 596 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 3) link_NAG-ASN : angle 1.53513 ( 9) link_BETA1-4 : bond 0.00160 ( 3) link_BETA1-4 : angle 2.94865 ( 9) hydrogen bonds : bond 0.05136 ( 419) hydrogen bonds : angle 4.63666 ( 1122) SS BOND : bond 0.00729 ( 24) SS BOND : angle 2.21299 ( 48) covalent geometry : bond 0.00472 (12519) covalent geometry : angle 0.66762 (17007) *********************** 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 235 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 2.187 Fit side-chains revert: symmetry clash REVERT: L 88 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7575 (t0) REVERT: A 71 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7215 (pt0) REVERT: A 112 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: A 140 LYS cc_start: 0.8942 (tttt) cc_final: 0.8489 (mtpp) REVERT: B 587 ARG cc_start: 0.8353 (mtt180) cc_final: 0.7992 (ttm110) REVERT: D 587 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7749 (ttm110) REVERT: D 595 GLN cc_start: 0.7322 (mm-40) cc_final: 0.7116 (mm110) REVERT: F 587 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7807 (ttm110) REVERT: C 84 LYS cc_start: 0.9075 (mttt) cc_final: 0.8740 (mtmt) REVERT: C 112 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: E 140 LYS cc_start: 0.8874 (tttt) cc_final: 0.8446 (mtpp) REVERT: P 56 ASP cc_start: 0.8686 (m-30) cc_final: 0.8417 (m-30) REVERT: P 91 GLU cc_start: 0.7959 (pm20) cc_final: 0.7593 (pm20) REVERT: P 112 ASP cc_start: 0.8690 (m-30) cc_final: 0.8477 (m-30) REVERT: Y 89 ARG cc_start: 0.7918 (ptp90) cc_final: 0.7630 (ptp90) REVERT: Y 91 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7553 (pm20) outliers start: 52 outliers final: 39 residues processed: 211 average time/residue: 1.6637 time to fit residues: 377.7179 Evaluate side-chains 225 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 71 GLU Chi-restraints excluded: chain A residue 112 GLU 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 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 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 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 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 61 ASP Chi-restraints excluded: chain Y residue 66 VAL 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 38 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 F 595 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.171764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134027 restraints weight = 13642.463| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.13 r_work: 0.3199 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12549 Z= 0.149 Angle : 0.633 11.159 17073 Z= 0.325 Chirality : 0.044 0.149 1851 Planarity : 0.004 0.044 2214 Dihedral : 4.928 26.447 1851 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.89 % Allowed : 19.24 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1554 helix: 0.63 (0.41), residues: 144 sheet: -0.07 (0.20), residues: 567 loop : -0.72 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 47 HIS 0.003 0.001 HIS C 154 PHE 0.014 0.001 PHE F 582 TYR 0.012 0.002 TYR F 517 ARG 0.010 0.001 ARG B 596 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 3) link_NAG-ASN : angle 1.25546 ( 9) link_BETA1-4 : bond 0.00316 ( 3) link_BETA1-4 : angle 2.74358 ( 9) hydrogen bonds : bond 0.04555 ( 419) hydrogen bonds : angle 4.58734 ( 1122) SS BOND : bond 0.00579 ( 24) SS BOND : angle 1.94280 ( 48) covalent geometry : bond 0.00349 (12519) covalent geometry : angle 0.62220 (17007) *********************** 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 239 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 88 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7401 (t0) REVERT: H 89 ARG cc_start: 0.7758 (ptp90) cc_final: 0.7231 (ptp90) REVERT: A 71 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: A 112 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: A 140 LYS cc_start: 0.8787 (tttt) cc_final: 0.8339 (mtpp) REVERT: B 587 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7753 (ttm110) REVERT: D 587 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7490 (ttm110) REVERT: F 587 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7591 (ttm110) REVERT: C 84 LYS cc_start: 0.8999 (mttt) cc_final: 0.8708 (mtmt) REVERT: C 112 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: E 140 LYS cc_start: 0.8755 (tttt) cc_final: 0.8333 (mtpp) REVERT: P 43 LYS cc_start: 0.7978 (mppt) cc_final: 0.7688 (mppt) REVERT: P 56 ASP cc_start: 0.8634 (m-30) cc_final: 0.8247 (m-30) REVERT: P 91 GLU cc_start: 0.7809 (pm20) cc_final: 0.7554 (pm20) REVERT: Y 43 LYS cc_start: 0.7801 (mppt) cc_final: 0.7556 (mppt) REVERT: Y 56 ASP cc_start: 0.8536 (m-30) cc_final: 0.8212 (m-30) outliers start: 50 outliers final: 42 residues processed: 218 average time/residue: 1.3279 time to fit residues: 312.5833 Evaluate side-chains 231 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 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 71 GLU Chi-restraints excluded: chain A residue 112 GLU 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 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 52 VAL Chi-restraints excluded: chain C residue 58 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 C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN 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 59 THR Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 66 VAL 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 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 7 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 117 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 48 optimal weight: 0.0970 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- 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 U 37 GLN D 595 GLN F 595 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** 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 = 0.3911 r_free = 0.3911 target = 0.172677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.134875 restraints weight = 13508.619| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.11 r_work: 0.3182 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12549 Z= 0.141 Angle : 0.623 11.087 17073 Z= 0.319 Chirality : 0.044 0.156 1851 Planarity : 0.004 0.039 2214 Dihedral : 4.863 26.136 1851 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.66 % Allowed : 19.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1554 helix: 0.72 (0.41), residues: 144 sheet: 0.03 (0.20), residues: 561 loop : -0.72 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 47 HIS 0.002 0.001 HIS C 154 PHE 0.013 0.001 PHE F 582 TYR 0.013 0.002 TYR F 517 ARG 0.007 0.001 ARG Y 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 3) link_NAG-ASN : angle 1.25332 ( 9) link_BETA1-4 : bond 0.00315 ( 3) link_BETA1-4 : angle 2.69423 ( 9) hydrogen bonds : bond 0.04441 ( 419) hydrogen bonds : angle 4.52224 ( 1122) SS BOND : bond 0.00565 ( 24) SS BOND : angle 1.91519 ( 48) covalent geometry : bond 0.00328 (12519) covalent geometry : angle 0.61226 (17007) ********************** 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 234 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: L 88 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7427 (t0) REVERT: H 89 ARG cc_start: 0.7771 (ptp90) cc_final: 0.7203 (ptp90) REVERT: A 71 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: A 112 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: A 140 LYS cc_start: 0.8788 (tttt) cc_final: 0.8333 (mtpp) REVERT: B 587 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7776 (ttm110) REVERT: U 57 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8720 (mtm180) REVERT: D 587 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7468 (ttm110) REVERT: F 587 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7576 (ttm110) REVERT: C 84 LYS cc_start: 0.8991 (mttt) cc_final: 0.8701 (mtmt) REVERT: C 112 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: E 140 LYS cc_start: 0.8755 (tttt) cc_final: 0.8335 (mtpp) REVERT: P 56 ASP cc_start: 0.8630 (m-30) cc_final: 0.8222 (m-30) REVERT: P 91 GLU cc_start: 0.7883 (pm20) cc_final: 0.7372 (pm20) REVERT: Y 56 ASP cc_start: 0.8486 (m-30) cc_final: 0.8179 (m-30) outliers start: 47 outliers final: 39 residues processed: 213 average time/residue: 1.3865 time to fit residues: 319.2229 Evaluate side-chains 228 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 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 71 GLU Chi-restraints excluded: chain A residue 112 GLU 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 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN 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 59 THR Chi-restraints excluded: chain P residue 61 ASP 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 61 ASP Chi-restraints excluded: chain Y residue 66 VAL 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 40 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 595 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.168445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130078 restraints weight = 13697.902| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.19 r_work: 0.3131 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3178 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= 0.187 Angle : 0.677 11.038 17073 Z= 0.348 Chirality : 0.046 0.176 1851 Planarity : 0.005 0.042 2214 Dihedral : 5.014 26.731 1851 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.66 % Allowed : 19.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1554 helix: 0.62 (0.40), residues: 144 sheet: -0.08 (0.20), residues: 567 loop : -0.77 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 47 HIS 0.003 0.001 HIS C 154 PHE 0.014 0.002 PHE A 225 TYR 0.014 0.002 TYR Y 97 ARG 0.007 0.001 ARG P 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 3) link_NAG-ASN : angle 1.45172 ( 9) link_BETA1-4 : bond 0.00217 ( 3) link_BETA1-4 : angle 2.89864 ( 9) hydrogen bonds : bond 0.04979 ( 419) hydrogen bonds : angle 4.57846 ( 1122) SS BOND : bond 0.00691 ( 24) SS BOND : angle 2.12159 ( 48) covalent geometry : bond 0.00449 (12519) covalent geometry : angle 0.66430 (17007) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9696.48 seconds wall clock time: 172 minutes 23.64 seconds (10343.64 seconds total)