Starting phenix.real_space_refine on Sat Oct 24 03:56:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s8j_10124/10_2026/6s8j_10124.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s8j_10124/10_2026/6s8j_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 { model { file = "/net/cci-nas-00/data/ceres_data/6s8j_10124/10_2026/6s8j_10124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s8j_10124/10_2026/6s8j_10124.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s8j_10124/10_2026/6s8j_10124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s8j_10124/10_2026/6s8j_10124.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6s8j_10124/10_2026/6s8j_10124.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s8j_10124/10_2026/6s8j_10124.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.194 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7728 2.51 5 N 2106 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12391 Number of models: 1 Model: "" Number of chains: 17 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 937 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Y" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Restraints were copied for chains: O, U, P, Y, C, E, D, F, I, J Time building chain proxies: 2.40, per 1000 atoms: 0.19 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 D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.04 Simple disulfide: pdb=" SG CYS D 609 " - pdb=" SG CYS C 53 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.04 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS E 53 " distance=2.08 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 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 108 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 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 22 " - pdb=" SG CYS Y 98 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 105 " - pdb=" SG CYS Y 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN D 563 " " NAG J 1 " - " ASN F 563 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 717.4 milliseconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2820 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 33 sheets defined 14.6% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.931A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.599A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.951A pdb=" N ILE B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.518A pdb=" N GLY B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 removed outlier: 3.700A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.931A pdb=" N GLU O 86 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 86 removed outlier: 3.932A pdb=" N GLU U 86 " --> pdb=" O ALA U 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.951A pdb=" N ILE D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.518A pdb=" N GLY D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.700A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.951A pdb=" N ILE F 542 " --> pdb=" O ALA F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.518A pdb=" N GLY F 557 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 3.700A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.599A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 84 removed outlier: 3.599A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 53 through 57 Processing helix chain 'Y' and resid 28 through 32 Processing helix chain 'Y' and resid 53 through 57 Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.254A pdb=" N GLN L 40 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.614A pdb=" N GLN L 101 " --> pdb=" O ASP L 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 60 through 62 removed outlier: 5.168A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.705A pdb=" N ALA A 42 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.705A pdb=" N ALA A 42 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA9, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AB1, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.388A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 601 through 602 removed outlier: 6.717A pdb=" N CYS B 601 " --> pdb=" O GLU F 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 610 through 611 Processing sheet with id=AB4, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.254A pdb=" N GLN O 40 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL O 49 " --> pdb=" O GLN O 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.614A pdb=" N GLN O 101 " --> pdb=" O ASP O 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 18 through 24 Processing sheet with id=AB7, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.254A pdb=" N GLN U 40 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL U 49 " --> pdb=" O GLN U 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.614A pdb=" N GLN U 101 " --> pdb=" O ASP U 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 18 through 24 Processing sheet with id=AC1, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AC2, first strand: chain 'D' and resid 580 through 581 removed outlier: 3.504A pdb=" N ASN C 98 " --> pdb=" O THR D 581 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C 42 " --> pdb=" O HIS C 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 580 through 581 removed outlier: 3.504A pdb=" N ASN C 98 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 610 through 611 Processing sheet with id=AC5, first strand: chain 'F' and resid 544 through 548 Processing sheet with id=AC6, first strand: chain 'F' and resid 580 through 581 removed outlier: 6.841A pdb=" N GLY E 36 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA E 42 " --> pdb=" O HIS E 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 580 through 581 Processing sheet with id=AC8, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC9, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.388A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AD2, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.388A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU E 112 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'P' and resid 60 through 62 removed outlier: 5.168A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'Y' and resid 60 through 62 removed outlier: 5.169A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.39 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: 6681 17.35 - 34.70: 505 34.70 - 52.04: 104 52.04 - 69.39: 21 69.39 - 86.74: 18 Dihedral angle restraints: 7329 sinusoidal: 2868 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 7326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1798 0.127 - 0.253: 47 0.253 - 0.380: 0 0.380 - 0.507: 0 0.507 - 0.634: 6 Chirality restraints: 1851 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.57e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.55e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.54e+02 ... (remaining 1848 not shown) Planarity restraints: 2217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 235 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" CD GLU A 235 " -0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU A 235 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU A 235 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 235 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" CD GLU C 235 " -0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU C 235 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU C 235 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 235 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" CD GLU E 235 " -0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU E 235 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU E 235 " 0.019 2.00e-02 2.50e+03 ... (remaining 2214 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 756 2.73 - 3.27: 11479 3.27 - 3.81: 18714 3.81 - 4.36: 24579 4.36 - 4.90: 42007 Nonbonded interactions: 97535 Sorted by model distance: nonbonded pdb=" NZ LYS E 114 " pdb=" OD2 ASP Y 56 " model vdw 2.185 3.120 nonbonded pdb=" O GLY Y 101 " pdb=" O HOH Y 301 " model vdw 2.218 3.040 nonbonded pdb=" OE2 GLU H 46 " pdb=" O HOH H 301 " model vdw 2.224 3.040 nonbonded pdb=" O GLY P 101 " pdb=" O HOH P 301 " model vdw 2.229 3.040 nonbonded pdb=" O GLY H 101 " pdb=" O HOH H 302 " model vdw 2.245 3.040 ... (remaining 97530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.960 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 13.262 85.274 4437 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.28 % Favored : 96.53 % Rotamer: Outliers : 3.27 % Allowed : 5.69 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1554 helix: 0.15 (0.41), residues: 144 sheet: 0.05 (0.21), residues: 555 loop : -0.86 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG C 54 TYR 0.021 0.003 TYR L 94 PHE 0.033 0.003 PHE H 70 TRP 0.015 0.002 TRP Y 114 HIS 0.027 0.005 HIS D 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.26 (12519) covalent geometry : angle 0.99578 / 0.54 (17007) SS BOND : bond 0.01439 / 0.83 ( 24) SS BOND : angle 3.13593 / 2.01 ( 48) hydrogen bonds : bond 0.13735 / 9.16 ( 419) hydrogen bonds : angle 6.78293 / 4.70 ( 1122) link_BETA1-4 : bond 0.06505 / 3.26 ( 3) link_BETA1-4 : angle 22.15334 / 12.95 ( 9) link_NAG-ASN : bond 0.00222 / 0.11 ( 3) link_NAG-ASN : angle 2.53806 / 1.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 0.461 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: 0.6674 (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: 0.7031 (m-30) cc_final: 0.6716 (m-30) REVERT: E 140 LYS cc_start: 0.8446 (tttt) cc_final: 0.8142 (mtpp) REVERT: Y 91 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6561 (pm20) outliers start: 42 outliers final: 6 residues processed: 307 average time/residue: 0.5483 time to fit residues: 183.5159 Evaluate side-chains 212 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4024 r_free = 0.4024 target = 0.183755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.148556 restraints weight = 14017.009| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.16 r_work: 0.3371 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12549 Z= 0.130 Angle : 0.669 13.167 17073 Z= 0.346 Chirality : 0.044 0.191 1851 Planarity : 0.005 0.042 2214 Dihedral : 5.374 48.463 1736 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.21 % Allowed : 13.94 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.19), residues: 1554 helix: 1.37 (0.44), residues: 144 sheet: 0.31 (0.20), residues: 576 loop : -0.87 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 54 TYR 0.014 0.001 TYR Y 82 PHE 0.013 0.001 PHE E 225 TRP 0.005 0.001 TRP B 597 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (12519) covalent geometry : angle 0.66066 / 0.34 (17007) SS BOND : bond 0.00423 / 0.25 ( 24) SS BOND : angle 1.58527 / 0.96 ( 48) hydrogen bonds : bond 0.04764 / 3.09 ( 419) hydrogen bonds : angle 5.15941 / 3.51 ( 1122) link_BETA1-4 : bond 0.00619 / 0.31 ( 3) link_BETA1-4 : angle 3.11127 / 1.60 ( 9) link_NAG-ASN : bond 0.00620 / 0.31 ( 3) link_NAG-ASN : angle 0.78052 / 0.50 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 239 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8275 (pttt) cc_final: 0.7992 (pttm) REVERT: L 75 SER cc_start: 0.8530 (p) cc_final: 0.8318 (p) REVERT: H 56 ASP cc_start: 0.8324 (m-30) cc_final: 0.7913 (m-30) REVERT: H 89 ARG cc_start: 0.7447 (ptp-170) cc_final: 0.7245 (ptp90) REVERT: H 91 GLU cc_start: 0.7346 (pm20) cc_final: 0.6941 (pm20) REVERT: A 140 LYS cc_start: 0.8585 (tttt) cc_final: 0.8073 (mtpp) REVERT: A 216 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7545 (p) REVERT: B 587 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7807 (ttm110) REVERT: B 604 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7318 (pp) REVERT: U 48 LYS cc_start: 0.8356 (pttt) cc_final: 0.8115 (pttm) REVERT: D 587 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7751 (ttm110) REVERT: F 587 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7194 (ttt180) REVERT: C 44 GLN cc_start: 0.6755 (tt0) cc_final: 0.6482 (tt0) REVERT: C 84 LYS cc_start: 0.8847 (mttt) cc_final: 0.8581 (mtpt) REVERT: C 106 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8041 (tp30) REVERT: C 112 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: C 150 ASP cc_start: 0.7374 (m-30) cc_final: 0.7167 (m-30) REVERT: E 140 LYS cc_start: 0.8624 (tttt) cc_final: 0.8260 (mtpp) REVERT: E 216 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8112 (p) REVERT: P 43 LYS cc_start: 0.8162 (mppt) cc_final: 0.7725 (mmtm) REVERT: P 91 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6815 (pm20) REVERT: Y 43 LYS cc_start: 0.7801 (mppt) cc_final: 0.7504 (mmtm) REVERT: Y 54 LYS cc_start: 0.7615 (tppt) cc_final: 0.7345 (tppp) REVERT: Y 91 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6917 (pm20) outliers start: 54 outliers final: 26 residues processed: 274 average time/residue: 0.5539 time to fit residues: 165.0069 Evaluate side-chains 239 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain 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 175 THR Chi-restraints excluded: chain E residue 46 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 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 85 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [142, 5, 18, 130, 151, 68, 39, 57, 52, 60, 73] chunk 142 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 31 ASN B 586 ASN B 595 GLN O 82 GLN D 567 GLN D 586 ASN D 595 GLN F 586 ASN F 595 GLN C 44 GLN C 221 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN P 31 ASN Y 31 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.173545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.135873 restraints weight = 13774.403| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.29 r_work: 0.3182 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12549 Z= 0.221 Angle : 0.751 13.030 17073 Z= 0.388 Chirality : 0.048 0.151 1851 Planarity : 0.005 0.037 2214 Dihedral : 5.263 36.484 1730 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.76 % Allowed : 14.25 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.19), residues: 1554 helix: 0.80 (0.42), residues: 144 sheet: 0.25 (0.19), residues: 606 loop : -0.92 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 54 TYR 0.015 0.002 TYR Y 97 PHE 0.018 0.002 PHE A 225 TRP 0.015 0.002 TRP Y 47 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (12519) covalent geometry : angle 0.73983 / 0.38 (17007) SS BOND : bond 0.00703 / 0.42 ( 24) SS BOND : angle 2.03598 / 1.22 ( 48) hydrogen bonds : bond 0.05632 / 3.64 ( 419) hydrogen bonds : angle 4.97943 / 3.35 ( 1122) link_BETA1-4 : bond 0.00317 / 0.16 ( 3) link_BETA1-4 : angle 3.14022 / 1.74 ( 9) link_NAG-ASN : bond 0.00286 / 0.14 ( 3) link_NAG-ASN : angle 1.93220 / 1.26 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 213 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8585 (pttt) cc_final: 0.8267 (pttm) REVERT: L 75 SER cc_start: 0.8844 (p) cc_final: 0.8637 (p) REVERT: H 54 LYS cc_start: 0.7608 (tppt) cc_final: 0.7388 (tptp) REVERT: A 45 VAL cc_start: 0.7284 (OUTLIER) cc_final: 0.6903 (t) REVERT: A 112 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: A 140 LYS cc_start: 0.8925 (tttt) cc_final: 0.8387 (mtpp) REVERT: A 216 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7728 (p) REVERT: B 587 ARG cc_start: 0.8380 (mtt180) cc_final: 0.8014 (ttm110) REVERT: U 48 LYS cc_start: 0.8601 (pttt) cc_final: 0.8345 (pttm) REVERT: U 57 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8610 (mtm180) REVERT: D 587 ARG cc_start: 0.8380 (mtt180) cc_final: 0.7801 (ttm110) REVERT: D 595 GLN cc_start: 0.7281 (mm-40) cc_final: 0.7031 (mm110) REVERT: F 587 ARG cc_start: 0.8326 (mtt180) cc_final: 0.8031 (ttm110) REVERT: C 44 GLN cc_start: 0.6809 (tt0) cc_final: 0.6416 (tt0) REVERT: C 71 GLU cc_start: 0.7781 (tt0) cc_final: 0.7410 (pt0) REVERT: C 84 LYS cc_start: 0.9043 (mttt) cc_final: 0.8757 (mtpt) REVERT: C 106 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8197 (tp30) REVERT: C 112 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: E 45 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.7219 (p) REVERT: E 71 GLU cc_start: 0.7800 (tt0) cc_final: 0.7456 (pt0) REVERT: E 112 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: E 140 LYS cc_start: 0.8840 (tttt) cc_final: 0.8396 (mtpp) REVERT: P 43 LYS cc_start: 0.8233 (mppt) cc_final: 0.7897 (mppt) REVERT: P 89 ARG cc_start: 0.7674 (ptp-170) cc_final: 0.7434 (ptp90) REVERT: P 91 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7132 (pm20) REVERT: Y 43 LYS cc_start: 0.7941 (mppt) cc_final: 0.7658 (mppt) REVERT: Y 89 ARG cc_start: 0.7440 (ptp-170) cc_final: 0.6967 (ptp90) REVERT: Y 91 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7263 (pm20) REVERT: Y 92 ASP cc_start: 0.7707 (m-30) cc_final: 0.7420 (m-30) outliers start: 74 outliers final: 46 residues processed: 259 average time/residue: 0.5860 time to fit residues: 164.2668 Evaluate side-chains 258 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 49 VAL 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 D residue 600 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain Y residue 6 GLU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 85 MET Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [132, 21, 24, 29, 28, 155, 75, 47, 99, 140, 0] chunk 132 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 31 ASN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN F 586 ASN ** 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 = 0.3920 r_free = 0.3920 target = 0.173594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135885 restraints weight = 13632.716| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.18 r_work: 0.3189 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2402 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= 0.163 Angle : 0.659 12.191 17073 Z= 0.340 Chirality : 0.045 0.154 1851 Planarity : 0.005 0.037 2214 Dihedral : 4.922 31.876 1726 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.76 % Allowed : 14.88 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.19), residues: 1554 helix: 0.76 (0.42), residues: 144 sheet: 0.15 (0.20), residues: 561 loop : -0.86 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 54 TYR 0.011 0.002 TYR E 137 PHE 0.014 0.002 PHE P 70 TRP 0.013 0.002 TRP H 47 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (12519) covalent geometry : angle 0.65001 / 0.34 (17007) SS BOND : bond 0.00568 / 0.33 ( 24) SS BOND : angle 1.68308 / 1.00 ( 48) hydrogen bonds : bond 0.04846 / 3.13 ( 419) hydrogen bonds : angle 4.78452 / 3.24 ( 1122) link_BETA1-4 : bond 0.00256 / 0.13 ( 3) link_BETA1-4 : angle 2.83433 / 1.51 ( 9) link_NAG-ASN : bond 0.00205 / 0.11 ( 3) link_NAG-ASN : angle 1.27775 / 0.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 197 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8579 (pttt) cc_final: 0.8288 (pttm) REVERT: L 75 SER cc_start: 0.8848 (p) cc_final: 0.8631 (p) REVERT: A 112 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: A 140 LYS cc_start: 0.8941 (tttt) cc_final: 0.8436 (mtpp) REVERT: A 216 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7729 (p) REVERT: B 587 ARG cc_start: 0.8365 (mtt180) cc_final: 0.8020 (ttm110) REVERT: B 595 GLN cc_start: 0.7310 (mm-40) cc_final: 0.7103 (mm110) REVERT: O 97 ARG cc_start: 0.8545 (ttp-170) cc_final: 0.8313 (mtm-85) REVERT: U 48 LYS cc_start: 0.8569 (pttt) cc_final: 0.8317 (pttm) REVERT: D 529 LEU cc_start: 0.8514 (mt) cc_final: 0.8314 (mt) REVERT: D 587 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7776 (ttm110) REVERT: D 595 GLN cc_start: 0.7244 (mm-40) cc_final: 0.7042 (mm110) REVERT: F 587 ARG cc_start: 0.8280 (mtt180) cc_final: 0.7319 (ttt90) REVERT: C 71 GLU cc_start: 0.7789 (tt0) cc_final: 0.7506 (pt0) REVERT: C 84 LYS cc_start: 0.9075 (mttt) cc_final: 0.8751 (mtmt) REVERT: C 106 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8244 (tp30) REVERT: C 112 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: E 112 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: E 140 LYS cc_start: 0.8851 (tttt) cc_final: 0.8406 (mtpp) REVERT: P 43 LYS cc_start: 0.8224 (mppt) cc_final: 0.7745 (mppt) REVERT: P 89 ARG cc_start: 0.7739 (ptp-170) cc_final: 0.7454 (ptp90) REVERT: P 91 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7176 (pm20) REVERT: Y 43 LYS cc_start: 0.7872 (mppt) cc_final: 0.7602 (mppt) REVERT: Y 89 ARG cc_start: 0.7668 (ptp-170) cc_final: 0.7263 (ptp90) REVERT: Y 91 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7428 (pm20) outliers start: 74 outliers final: 47 residues processed: 245 average time/residue: 0.5578 time to fit residues: 148.3258 Evaluate side-chains 238 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 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 600 THR Chi-restraints excluded: chain F residue 552 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 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 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 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain Y residue 6 GLU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [129, 4, 8, 54, 32, 117, 151, 19, 141, 33, 20] chunk 129 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 8 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 31 ASN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.172478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134609 restraints weight = 13610.153| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.19 r_work: 0.3183 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12549 Z= 0.166 Angle : 0.652 11.957 17073 Z= 0.337 Chirality : 0.045 0.141 1851 Planarity : 0.005 0.040 2214 Dihedral : 4.859 26.368 1726 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 6.23 % Allowed : 14.64 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.19), residues: 1554 helix: 0.69 (0.41), residues: 144 sheet: 0.10 (0.20), residues: 561 loop : -0.79 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 130 TYR 0.012 0.002 TYR Y 97 PHE 0.014 0.002 PHE A 225 TRP 0.015 0.002 TRP Y 47 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (12519) covalent geometry : angle 0.64293 / 0.33 (17007) SS BOND : bond 0.00603 / 0.36 ( 24) SS BOND : angle 1.68934 / 0.99 ( 48) hydrogen bonds : bond 0.04870 / 3.15 ( 419) hydrogen bonds : angle 4.70530 / 3.19 ( 1122) link_BETA1-4 : bond 0.00227 / 0.12 ( 3) link_BETA1-4 : angle 2.75038 / 1.50 ( 9) link_NAG-ASN : bond 0.00125 / 0.06 ( 3) link_NAG-ASN : angle 1.31977 / 0.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 195 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8586 (pttt) cc_final: 0.8277 (pttm) REVERT: L 75 SER cc_start: 0.8837 (p) cc_final: 0.8626 (p) REVERT: H 56 ASP cc_start: 0.8727 (m-30) cc_final: 0.8512 (m-30) REVERT: A 112 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: A 140 LYS cc_start: 0.8938 (tttt) cc_final: 0.8459 (mtpp) REVERT: A 216 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7763 (p) REVERT: B 587 ARG cc_start: 0.8374 (mtt180) cc_final: 0.8032 (ttm110) REVERT: U 48 LYS cc_start: 0.8635 (pttt) cc_final: 0.8367 (pttm) REVERT: D 587 ARG cc_start: 0.8360 (mtt180) cc_final: 0.7775 (ttm110) REVERT: F 587 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7331 (mtp85) REVERT: C 71 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7521 (pt0) REVERT: C 84 LYS cc_start: 0.9079 (mttt) cc_final: 0.8742 (mtmt) REVERT: C 106 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8118 (tp30) REVERT: C 112 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8258 (mt-10) REVERT: E 112 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: E 140 LYS cc_start: 0.8843 (tttt) cc_final: 0.8398 (mtpp) REVERT: P 43 LYS cc_start: 0.8182 (mppt) cc_final: 0.7745 (mppt) REVERT: P 89 ARG cc_start: 0.7830 (ptp-170) cc_final: 0.7572 (ptp90) REVERT: P 91 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7214 (pm20) REVERT: Y 43 LYS cc_start: 0.7864 (mppt) cc_final: 0.7452 (mppt) REVERT: Y 68 ASP cc_start: 0.7561 (m-30) cc_final: 0.7360 (m-30) REVERT: Y 91 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7396 (pm20) outliers start: 80 outliers final: 49 residues processed: 246 average time/residue: 0.5607 time to fit residues: 149.8688 Evaluate side-chains 241 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 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 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Y residue 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: [147, 127, 23, 60, 29, 1, 139, 132, 95, 21, 62] chunk 147 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 586 ASN F 595 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Y 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.172164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.134588 restraints weight = 13610.665| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.22 r_work: 0.3164 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12549 Z= 0.215 Angle : 0.705 11.453 17073 Z= 0.364 Chirality : 0.047 0.143 1851 Planarity : 0.005 0.044 2214 Dihedral : 4.999 27.490 1726 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.53 % Allowed : 15.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1554 helix: 0.45 (0.40), residues: 144 sheet: -0.05 (0.20), residues: 567 loop : -0.84 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 130 TYR 0.014 0.002 TYR Y 97 PHE 0.016 0.002 PHE A 225 TRP 0.018 0.002 TRP Y 47 HIS 0.008 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.21 (12519) covalent geometry : angle 0.69050 / 0.36 (17007) SS BOND : bond 0.00737 / 0.45 ( 24) SS BOND : angle 2.44046 / 1.42 ( 48) hydrogen bonds : bond 0.05387 / 3.46 ( 419) hydrogen bonds : angle 4.74368 / 3.21 ( 1122) link_BETA1-4 : bond 0.00038 / 0.02 ( 3) link_BETA1-4 : angle 2.92397 / 1.58 ( 9) link_NAG-ASN : bond 0.00127 / 0.06 ( 3) link_NAG-ASN : angle 1.55087 / 0.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 193 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 LYS cc_start: 0.8600 (pttt) cc_final: 0.8287 (pttm) REVERT: L 75 SER cc_start: 0.8821 (p) cc_final: 0.8621 (p) REVERT: H 56 ASP cc_start: 0.8769 (m-30) cc_final: 0.8567 (m-30) REVERT: A 112 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: A 140 LYS cc_start: 0.8956 (tttt) cc_final: 0.8494 (mtpp) REVERT: A 216 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7775 (p) REVERT: B 587 ARG cc_start: 0.8394 (mtt180) cc_final: 0.8031 (ttm110) REVERT: U 48 LYS cc_start: 0.8649 (pttt) cc_final: 0.8377 (pttm) REVERT: D 587 ARG cc_start: 0.8348 (mtt180) cc_final: 0.7759 (ttm110) REVERT: D 595 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7152 (mm110) REVERT: F 587 ARG cc_start: 0.8287 (mtt180) cc_final: 0.7358 (mtp85) REVERT: C 71 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7542 (pt0) REVERT: C 84 LYS cc_start: 0.9084 (mttt) cc_final: 0.8741 (mtmt) REVERT: C 106 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8128 (tp30) REVERT: C 112 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8219 (mt-10) REVERT: C 140 LYS cc_start: 0.8940 (tttt) cc_final: 0.8486 (mtpp) REVERT: C 156 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8253 (mm-30) REVERT: E 112 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: E 140 LYS cc_start: 0.8873 (tttt) cc_final: 0.8425 (mtpp) REVERT: E 156 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8250 (mm-30) REVERT: P 43 LYS cc_start: 0.8162 (mppt) cc_final: 0.7827 (mppt) REVERT: P 56 ASP cc_start: 0.8673 (m-30) cc_final: 0.8439 (m-30) REVERT: P 89 ARG cc_start: 0.7908 (ptp-170) cc_final: 0.7696 (ptp90) REVERT: P 91 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7345 (pm20) REVERT: P 112 ASP cc_start: 0.8588 (m-30) cc_final: 0.8353 (m-30) REVERT: Y 48 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7903 (p) REVERT: Y 68 ASP cc_start: 0.7625 (m-30) cc_final: 0.7418 (m-30) REVERT: Y 91 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7587 (pm20) outliers start: 71 outliers final: 50 residues processed: 236 average time/residue: 0.5618 time to fit residues: 144.2582 Evaluate side-chains 246 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 75 SER Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 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 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 61 ASP Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 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 81 LEU Chi-restraints excluded: chain Y residue 105 CYS Chi-restraints excluded: chain Y residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [107, 111, 128, 144, 60, 49, 136, 5, 80, 58, 139] chunk 107 optimal weight: 0.0070 chunk 111 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 56 ASN H 31 ASN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN F 586 ASN F 595 GLN C 188 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.174097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136346 restraints weight = 13645.363| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.15 r_work: 0.3224 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12549 Z= 0.111 Angle : 0.581 11.381 17073 Z= 0.300 Chirality : 0.043 0.151 1851 Planarity : 0.004 0.036 2214 Dihedral : 4.627 25.977 1726 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.05 % Allowed : 17.68 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.20), residues: 1554 helix: 0.76 (0.41), residues: 144 sheet: 0.00 (0.20), residues: 567 loop : -0.68 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 130 TYR 0.010 0.001 TYR F 517 PHE 0.011 0.001 PHE F 582 TRP 0.009 0.001 TRP Y 47 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (12519) covalent geometry : angle 0.57085 / 0.30 (17007) SS BOND : bond 0.00451 / 0.27 ( 24) SS BOND : angle 1.78667 / 1.03 ( 48) hydrogen bonds : bond 0.04079 / 2.65 ( 419) hydrogen bonds : angle 4.62957 / 3.15 ( 1122) link_BETA1-4 : bond 0.00387 / 0.20 ( 3) link_BETA1-4 : angle 2.40216 / 1.27 ( 9) link_NAG-ASN : bond 0.00653 / 0.33 ( 3) link_NAG-ASN : angle 0.96778 / 0.60 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 75 SER cc_start: 0.8619 (p) cc_final: 0.8419 (p) REVERT: H 56 ASP cc_start: 0.8609 (m-30) cc_final: 0.8382 (m-30) REVERT: A 112 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: A 140 LYS cc_start: 0.8754 (tttt) cc_final: 0.8290 (mtpp) REVERT: B 587 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7744 (ttm110) REVERT: U 48 LYS cc_start: 0.8533 (pttt) cc_final: 0.8263 (pttm) REVERT: D 587 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7511 (ttm110) REVERT: F 587 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7144 (ttt90) REVERT: C 84 LYS cc_start: 0.8982 (mttt) cc_final: 0.8685 (mtmt) REVERT: C 112 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: E 112 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: E 140 LYS cc_start: 0.8731 (tttt) cc_final: 0.8303 (mtpp) REVERT: P 43 LYS cc_start: 0.8069 (mppt) cc_final: 0.7705 (mppt) REVERT: P 56 ASP cc_start: 0.8598 (m-30) cc_final: 0.8383 (m-30) REVERT: P 91 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7207 (pm20) REVERT: Y 43 LYS cc_start: 0.7781 (mppt) cc_final: 0.7510 (mppt) REVERT: Y 56 ASP cc_start: 0.8479 (m-30) cc_final: 0.8148 (m-30) REVERT: Y 91 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7429 (pm20) outliers start: 52 outliers final: 30 residues processed: 232 average time/residue: 0.5946 time to fit residues: 149.4189 Evaluate side-chains 224 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 105 CYS Chi-restraints excluded: chain A residue 84 LYS 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 D residue 600 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 44 GLN 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 55 SER Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain Y residue 6 GLU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 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: [0, 51, 150, 114, 102, 30, 105, 41, 40, 153, 18] chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN B 595 GLN U 37 GLN D 567 GLN D 595 GLN F 586 ASN F 595 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.171619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133737 restraints weight = 13587.841| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.18 r_work: 0.3173 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12549 Z= 0.173 Angle : 0.652 11.272 17073 Z= 0.337 Chirality : 0.045 0.143 1851 Planarity : 0.005 0.042 2214 Dihedral : 4.764 26.378 1725 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.97 % Allowed : 17.99 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1554 helix: 0.64 (0.40), residues: 144 sheet: -0.04 (0.20), residues: 567 loop : -0.70 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 596 TYR 0.013 0.002 TYR Y 97 PHE 0.014 0.002 PHE A 225 TRP 0.015 0.002 TRP Y 47 HIS 0.003 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (12519) covalent geometry : angle 0.63997 / 0.33 (17007) SS BOND : bond 0.00681 / 0.42 ( 24) SS BOND : angle 2.08598 / 1.21 ( 48) hydrogen bonds : bond 0.04844 / 3.12 ( 419) hydrogen bonds : angle 4.57929 / 3.10 ( 1122) link_BETA1-4 : bond 0.00173 / 0.09 ( 3) link_BETA1-4 : angle 2.67403 / 1.45 ( 9) link_NAG-ASN : bond 0.00077 / 0.04 ( 3) link_NAG-ASN : angle 1.35071 / 0.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 88 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7563 (t0) REVERT: H 56 ASP cc_start: 0.8751 (m-30) cc_final: 0.8494 (m-30) REVERT: A 112 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: A 140 LYS cc_start: 0.8948 (tttt) cc_final: 0.8487 (mtpp) REVERT: B 587 ARG cc_start: 0.8360 (mtt180) cc_final: 0.8021 (ttm110) REVERT: U 48 LYS cc_start: 0.8632 (pttt) cc_final: 0.8367 (pttm) REVERT: D 587 ARG cc_start: 0.8345 (mtt180) cc_final: 0.7770 (ttm110) REVERT: D 595 GLN cc_start: 0.7339 (mm-40) cc_final: 0.7120 (mm110) REVERT: F 587 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7364 (mtp85) REVERT: C 84 LYS cc_start: 0.9077 (mttt) cc_final: 0.8751 (mtmt) REVERT: C 112 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: E 112 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: E 140 LYS cc_start: 0.8880 (tttt) cc_final: 0.8425 (mtpp) REVERT: P 56 ASP cc_start: 0.8716 (m-30) cc_final: 0.8490 (m-30) REVERT: Y 56 ASP cc_start: 0.8580 (m-30) cc_final: 0.8267 (m-30) REVERT: Y 91 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7353 (pm20) outliers start: 51 outliers final: 42 residues processed: 210 average time/residue: 0.6044 time to fit residues: 137.2236 Evaluate side-chains 226 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 84 LYS 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 600 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 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN 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 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [79, 143, 46, 64, 92, 23, 0, 146, 30, 144, 140] chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 31 ASN ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.167849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129886 restraints weight = 13668.489| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.22 r_work: 0.3131 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12549 Z= 0.251 Angle : 0.738 11.139 17073 Z= 0.381 Chirality : 0.049 0.169 1851 Planarity : 0.005 0.046 2214 Dihedral : 5.072 28.149 1725 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.13 % Allowed : 18.22 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.19), residues: 1554 helix: 0.34 (0.39), residues: 144 sheet: -0.13 (0.20), residues: 567 loop : -0.94 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 596 TYR 0.016 0.003 TYR Y 97 PHE 0.016 0.002 PHE A 225 TRP 0.018 0.003 TRP Y 47 HIS 0.004 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.25 (12519) covalent geometry : angle 0.72409 / 0.38 (17007) SS BOND : bond 0.00847 / 0.52 ( 24) SS BOND : angle 2.41944 / 1.40 ( 48) hydrogen bonds : bond 0.05748 / 3.68 ( 419) hydrogen bonds : angle 4.73010 / 3.20 ( 1122) link_BETA1-4 : bond 0.00033 / 0.02 ( 3) link_BETA1-4 : angle 3.01230 / 1.63 ( 9) link_NAG-ASN : bond 0.00173 / 0.08 ( 3) link_NAG-ASN : angle 1.70018 / 1.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 88 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7610 (t0) REVERT: H 56 ASP cc_start: 0.8787 (m-30) cc_final: 0.8562 (m-30) REVERT: A 112 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: A 140 LYS cc_start: 0.8958 (tttt) cc_final: 0.8496 (mtpp) REVERT: B 587 ARG cc_start: 0.8360 (mtt180) cc_final: 0.7977 (ttm110) REVERT: D 587 ARG cc_start: 0.8326 (mtt180) cc_final: 0.7746 (ttm110) REVERT: D 595 GLN cc_start: 0.7342 (mm-40) cc_final: 0.7120 (mm110) REVERT: F 587 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7377 (ttt180) REVERT: C 84 LYS cc_start: 0.9088 (mttt) cc_final: 0.8730 (mtmt) REVERT: C 112 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: C 140 LYS cc_start: 0.8960 (tttt) cc_final: 0.8500 (mtpp) REVERT: E 112 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: E 140 LYS cc_start: 0.8898 (tttt) cc_final: 0.8435 (mtpp) REVERT: P 43 LYS cc_start: 0.8014 (mppt) cc_final: 0.7398 (mmtm) REVERT: P 56 ASP cc_start: 0.8744 (m-30) cc_final: 0.8515 (m-30) REVERT: Y 43 LYS cc_start: 0.7909 (mppt) cc_final: 0.7611 (mppt) REVERT: Y 56 ASP cc_start: 0.8678 (m-30) cc_final: 0.8391 (m-30) REVERT: Y 91 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7369 (pm20) outliers start: 53 outliers final: 44 residues processed: 216 average time/residue: 0.6189 time to fit residues: 144.5136 Evaluate side-chains 232 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 84 LYS 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 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 105 CYS Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 51 ILE 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: [62, 21, 153, 102, 20, 28, 51, 25, 135, 131, 16] chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3916 r_free = 0.3916 target = 0.173160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135466 restraints weight = 13574.985| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.07 r_work: 0.3178 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12549 Z= 0.122 Angle : 0.605 11.173 17073 Z= 0.313 Chirality : 0.044 0.160 1851 Planarity : 0.004 0.040 2214 Dihedral : 4.695 26.426 1725 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.35 % Allowed : 19.47 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1554 helix: 0.65 (0.40), residues: 144 sheet: -0.04 (0.20), residues: 567 loop : -0.77 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 89 TYR 0.012 0.001 TYR F 517 PHE 0.012 0.001 PHE F 582 TRP 0.011 0.001 TRP Y 47 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (12519) covalent geometry : angle 0.59503 / 0.31 (17007) SS BOND : bond 0.00498 / 0.30 ( 24) SS BOND : angle 1.80154 / 1.03 ( 48) hydrogen bonds : bond 0.04254 / 2.75 ( 419) hydrogen bonds : angle 4.57322 / 3.10 ( 1122) link_BETA1-4 : bond 0.00441 / 0.22 ( 3) link_BETA1-4 : angle 2.43466 / 1.29 ( 9) link_NAG-ASN : bond 0.00454 / 0.23 ( 3) link_NAG-ASN : angle 1.02475 / 0.63 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 88 ASP cc_start: 0.7910 (m-30) cc_final: 0.7509 (t0) REVERT: H 56 ASP cc_start: 0.8679 (m-30) cc_final: 0.8413 (m-30) REVERT: A 112 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: A 140 LYS cc_start: 0.8922 (tttt) cc_final: 0.8464 (mtpp) REVERT: B 587 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7949 (ttm110) REVERT: D 587 ARG cc_start: 0.8314 (mtt180) cc_final: 0.7733 (ttm110) REVERT: D 595 GLN cc_start: 0.7292 (mm-40) cc_final: 0.7073 (mm110) REVERT: F 587 ARG cc_start: 0.8279 (mtt180) cc_final: 0.7338 (mtp85) REVERT: C 84 LYS cc_start: 0.9068 (mttt) cc_final: 0.8730 (mtmt) REVERT: C 112 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: E 112 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: E 140 LYS cc_start: 0.8885 (tttt) cc_final: 0.8443 (mtpp) REVERT: P 43 LYS cc_start: 0.7964 (mppt) cc_final: 0.7697 (mppt) REVERT: Y 56 ASP cc_start: 0.8544 (m-30) cc_final: 0.8255 (m-30) outliers start: 43 outliers final: 35 residues processed: 211 average time/residue: 0.6041 time to fit residues: 137.8432 Evaluate side-chains 220 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 O residue 108 THR Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain U residue 88 ASP 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 175 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 85 MET 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: [147, 10, 108, 54, 79, 26, 134, 29, 42, 96, 39] chunk 147 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 96 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN F 586 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.176826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139671 restraints weight = 13459.615| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.06 r_work: 0.3239 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12549 Z= 0.106 Angle : 0.572 11.167 17073 Z= 0.294 Chirality : 0.043 0.168 1851 Planarity : 0.004 0.040 2214 Dihedral : 4.455 25.504 1725 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.88 % Allowed : 20.09 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1554 helix: 0.89 (0.41), residues: 144 sheet: 0.09 (0.21), residues: 567 loop : -0.62 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 89 TYR 0.014 0.001 TYR F 517 PHE 0.010 0.001 PHE F 582 TRP 0.008 0.001 TRP P 47 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (12519) covalent geometry : angle 0.56411 / 0.29 (17007) SS BOND : bond 0.00429 / 0.26 ( 24) SS BOND : angle 1.63607 / 0.94 ( 48) hydrogen bonds : bond 0.03797 / 2.46 ( 419) hydrogen bonds : angle 4.42258 / 3.01 ( 1122) link_BETA1-4 : bond 0.00412 / 0.21 ( 3) link_BETA1-4 : angle 2.23782 / 1.21 ( 9) link_NAG-ASN : bond 0.00356 / 0.18 ( 3) link_NAG-ASN : angle 0.91628 / 0.57 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4379.08 seconds wall clock time: 75 minutes 9.75 seconds (4509.75 seconds total)