Starting phenix.real_space_refine on Sat Jul 4 00:21:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tp6_41468/07_2026/8tp6_41468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp6_41468/07_2026/8tp6_41468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8tp6_41468/07_2026/8tp6_41468.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tp6_41468/07_2026/8tp6_41468.cif" model { file = "/net/cci-nas-00/data/ceres_data/8tp6_41468/07_2026/8tp6_41468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp6_41468/07_2026/8tp6_41468.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tp6_41468/07_2026/8tp6_41468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp6_41468/07_2026/8tp6_41468.map" } resolution = 3.1 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= -0.000 sd= 0.045 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 96 5.16 5 C 10626 2.51 5 N 2864 2.21 5 O 3422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17008 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3806 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 19, 'TRANS': 460} Chain breaks: 1 Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "B" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3806 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 19, 'TRANS': 460} Chain breaks: 1 Chain: "C" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "D" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "E" Number of atoms: 3801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3801 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 19, 'TRANS': 459} Chain breaks: 1 Chain: "F" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "P" 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: "U" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Y" 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: "d" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "h" 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.60, per 1000 atoms: 0.21 Number of scatterers: 17008 At special positions: 0 Unit cell: (121.9, 124.2, 166.75, 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 96 16.00 O 3422 8.00 N 2864 7.00 C 10626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.05 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.05 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E 466 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.05 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.02 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 477 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG P 1 " - " NAG P 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG Y 1 " - " NAG Y 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG h 1 " - " NAG h 2 " BETA1-6 " NAG K 1 " - " FUC K 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 4 " " NAG d 1 " - " FUC d 4 " NAG-ASN " NAG A 501 " - " ASN A 21 " " NAG A 502 " - " ASN A 33 " " NAG A 503 " - " ASN A 483 " " NAG B 501 " - " ASN B 21 " " NAG B 502 " - " ASN B 33 " " NAG B 503 " - " ASN B 483 " " NAG E 501 " - " ASN E 21 " " NAG E 502 " - " ASN E 33 " " NAG E 503 " - " ASN E 483 " " NAG K 1 " - " ASN A 169 " " NAG P 1 " - " ASN A 289 " " NAG U 1 " - " ASN B 169 " " NAG Y 1 " - " ASN B 289 " " NAG d 1 " - " ASN E 169 " " NAG h 1 " - " ASN E 289 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 695.9 milliseconds 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3874 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 51 sheets defined 19.6% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.598A pdb=" N SER A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A 114 " --> pdb=" O HIS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 127 removed outlier: 3.803A pdb=" N TRP A 127 " --> pdb=" O LYS A 125a" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 366 through 387 Processing helix chain 'A' and resid 403 through 456 removed outlier: 4.025A pdb=" N LEU A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.112A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.598A pdb=" N SER B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER B 114 " --> pdb=" O HIS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 removed outlier: 3.804A pdb=" N TRP B 127 " --> pdb=" O LYS B 125a" (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 403 through 456 removed outlier: 4.025A pdb=" N LEU B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.112A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 104 through 114 removed outlier: 3.598A pdb=" N SER E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER E 114 " --> pdb=" O HIS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 127 removed outlier: 3.803A pdb=" N TRP E 127 " --> pdb=" O LYS E 125a" (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'E' and resid 366 through 387 Processing helix chain 'E' and resid 403 through 456 removed outlier: 4.025A pdb=" N LEU E 409 " --> pdb=" O ARG E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 Processing helix chain 'E' and resid 487 through 491 Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.112A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.468A pdb=" N GLU A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.315A pdb=" N LEU A 51 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 5.949A pdb=" N LEU A 59 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 102 removed outlier: 7.873A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.225A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 9.700A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 168 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288 removed outlier: 3.842A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.943A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG H 38 " --> pdb=" O CYS H 47 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N CYS H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.823A pdb=" N MET H 96 " --> pdb=" O PHE H 100D" (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE H 100D" --> pdb=" O MET H 96 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE H 98 " --> pdb=" O ASP H 100B" (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP H 100B" --> pdb=" O PHE H 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.603A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.603A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR L 97 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AC1, first strand: chain 'B' and resid 24 through 26 removed outlier: 4.467A pdb=" N GLU B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.314A pdb=" N LEU B 51 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 59 through 60 removed outlier: 5.950A pdb=" N LEU B 59 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AC7, first strand: chain 'B' and resid 100 through 102 removed outlier: 7.874A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.225A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 164 through 168 Processing sheet with id=AD1, first strand: chain 'B' and resid 286 through 288 removed outlier: 3.842A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.943A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG C 38 " --> pdb=" O CYS C 47 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N CYS C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.823A pdb=" N MET C 96 " --> pdb=" O PHE C 100D" (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE C 100D" --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE C 98 " --> pdb=" O ASP C 100B" (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP C 100B" --> pdb=" O PHE C 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.604A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.604A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR D 97 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 364 through 365 Processing sheet with id=AD9, first strand: chain 'E' and resid 24 through 26 removed outlier: 4.467A pdb=" N GLU E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AE2, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.314A pdb=" N LEU E 51 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 59 through 60 removed outlier: 5.949A pdb=" N LEU E 59 " --> pdb=" O MET E 88 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE E 87 " --> pdb=" O MET E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AE6, first strand: chain 'E' and resid 100 through 102 removed outlier: 7.874A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.226A pdb=" N ALA E 138 " --> pdb=" O ASN E 144 " (cutoff:3.500A) removed outlier: 9.700A pdb=" N ASN E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 164 through 168 Processing sheet with id=AE9, first strand: chain 'E' and resid 286 through 288 removed outlier: 3.842A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.944A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG F 38 " --> pdb=" O CYS F 47 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N CYS F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.824A pdb=" N MET F 96 " --> pdb=" O PHE F 100D" (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE F 100D" --> pdb=" O MET F 96 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE F 98 " --> pdb=" O ASP F 100B" (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP F 100B" --> pdb=" O PHE F 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.604A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.604A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR G 97 " --> pdb=" O GLU G 90 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 1899 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: 2.77 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4469 1.33 - 1.46: 5295 1.46 - 1.60: 7442 1.60 - 1.73: 33 1.73 - 1.87: 132 Bond restraints: 17371 Sorted by residual: bond pdb=" CA VAL A 115 " pdb=" C VAL A 115 " ideal model delta sigma weight residual 1.526 1.436 0.090 9.00e-03 1.23e+04 9.94e+01 bond pdb=" CA VAL E 115 " pdb=" C VAL E 115 " ideal model delta sigma weight residual 1.526 1.437 0.089 9.00e-03 1.23e+04 9.87e+01 bond pdb=" CA VAL B 115 " pdb=" C VAL B 115 " ideal model delta sigma weight residual 1.526 1.437 0.089 9.00e-03 1.23e+04 9.87e+01 bond pdb=" CB HIS A 354 " pdb=" CG HIS A 354 " ideal model delta sigma weight residual 1.497 1.387 0.110 1.40e-02 5.10e+03 6.16e+01 bond pdb=" CB HIS E 354 " pdb=" CG HIS E 354 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.09e+01 ... (remaining 17366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 20314 2.43 - 4.86: 2732 4.86 - 7.29: 408 7.29 - 9.71: 68 9.71 - 12.14: 12 Bond angle restraints: 23534 Sorted by residual: angle pdb=" CA PHE B 118 " pdb=" CB PHE B 118 " pdb=" CG PHE B 118 " ideal model delta sigma weight residual 113.80 124.92 -11.12 1.00e+00 1.00e+00 1.24e+02 angle pdb=" CA PHE A 118 " pdb=" CB PHE A 118 " pdb=" CG PHE A 118 " ideal model delta sigma weight residual 113.80 124.92 -11.12 1.00e+00 1.00e+00 1.24e+02 angle pdb=" CA PHE E 118 " pdb=" CB PHE E 118 " pdb=" CG PHE E 118 " ideal model delta sigma weight residual 113.80 124.91 -11.11 1.00e+00 1.00e+00 1.24e+02 angle pdb=" C GLY C 8 " pdb=" N PRO C 9 " pdb=" CA PRO C 9 " ideal model delta sigma weight residual 120.03 129.23 -9.20 9.90e-01 1.02e+00 8.64e+01 angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 120.03 129.19 -9.16 9.90e-01 1.02e+00 8.55e+01 ... (remaining 23529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 9765 17.06 - 34.12: 284 34.12 - 51.18: 58 51.18 - 68.24: 51 68.24 - 85.30: 12 Dihedral angle restraints: 10170 sinusoidal: 4089 harmonic: 6081 Sorted by residual: dihedral pdb=" C PHE B 118 " pdb=" N PHE B 118 " pdb=" CA PHE B 118 " pdb=" CB PHE B 118 " ideal model delta harmonic sigma weight residual -122.60 -111.56 -11.04 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" C PHE A 118 " pdb=" N PHE A 118 " pdb=" CA PHE A 118 " pdb=" CB PHE A 118 " ideal model delta harmonic sigma weight residual -122.60 -111.60 -11.00 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" C PHE E 118 " pdb=" N PHE E 118 " pdb=" CA PHE E 118 " pdb=" CB PHE E 118 " ideal model delta harmonic sigma weight residual -122.60 -111.61 -10.99 0 2.50e+00 1.60e-01 1.93e+01 ... (remaining 10167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1848 0.103 - 0.205: 622 0.205 - 0.308: 121 0.308 - 0.410: 24 0.410 - 0.513: 27 Chirality restraints: 2642 Sorted by residual: chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.66e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.50e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.39e+01 ... (remaining 2639 not shown) Planarity restraints: 3023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 33 " -0.057 2.00e-02 2.50e+03 5.91e-02 4.37e+01 pdb=" CG ASN E 33 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN E 33 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN E 33 " 0.091 2.00e-02 2.50e+03 pdb=" C1 NAG E 502 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 33 " 0.057 2.00e-02 2.50e+03 5.91e-02 4.37e+01 pdb=" CG ASN B 33 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 33 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 33 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 33 " -0.057 2.00e-02 2.50e+03 5.91e-02 4.36e+01 pdb=" CG ASN A 33 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 33 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 33 " 0.091 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.071 2.00e-02 2.50e+03 ... (remaining 3020 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5291 2.84 - 3.36: 15098 3.36 - 3.87: 29050 3.87 - 4.39: 34667 4.39 - 4.90: 57201 Nonbonded interactions: 141307 Sorted by model distance: nonbonded pdb=" N ILE B 335 " pdb=" N ALA B 336 " model vdw 2.326 2.560 nonbonded pdb=" C ALA B 334 " pdb=" N ALA B 336 " model vdw 2.385 3.350 nonbonded pdb=" OD2 ASP A 41 " pdb=" NZ LYS A 45 " model vdw 2.393 3.120 nonbonded pdb=" OD2 ASP B 41 " pdb=" NZ LYS B 45 " model vdw 2.393 3.120 nonbonded pdb=" OD2 ASP E 41 " pdb=" NZ LYS E 45 " model vdw 2.393 3.120 ... (remaining 141302 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 324 or resid 335 through 503)) selection = (chain 'B' and (resid 11 through 324 or resid 335 through 503)) selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'U' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'Y' selection = chain 'h' } 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: 2.140 Set stop_for_unknowns flag: 0.010 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.170 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.021 0.115 17422 Z= 1.143 Angle : 1.786 12.143 23663 Z= 1.186 Chirality : 0.114 0.513 2642 Planarity : 0.009 0.043 3008 Dihedral : 10.443 85.300 6224 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 3.57 % 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: 1.02 (0.17), residues: 2102 helix: 0.52 (0.24), residues: 341 sheet: 1.20 (0.20), residues: 561 loop : 0.61 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 456 TYR 0.068 0.010 TYR E 448 PHE 0.052 0.008 PHE E 118 TRP 0.033 0.008 TRP L 35 HIS 0.011 0.003 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.02101 / 1.14 (17371) covalent geometry : angle 1.77456 / 1.19 (23534) SS BOND : bond 0.00712 / 0.46 ( 24) SS BOND : angle 2.34758 / 1.51 ( 48) hydrogen bonds : bond 0.13767 / 9.33 ( 672) hydrogen bonds : angle 7.69596 / 5.42 ( 1899) link_BETA1-4 : bond 0.07358 / 4.15 ( 9) link_BETA1-4 : angle 5.01980 / 3.32 ( 27) link_BETA1-6 : bond 0.04691 / 2.35 ( 3) link_BETA1-6 : angle 3.04491 / 1.39 ( 9) link_NAG-ASN : bond 0.08060 / 4.78 ( 15) link_NAG-ASN : angle 2.87410 / 1.91 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 LYS cc_start: 0.8461 (pttt) cc_final: 0.8220 (ptmm) REVERT: B 460 LYS cc_start: 0.8515 (pttt) cc_final: 0.8255 (ptmm) REVERT: E 474 ASP cc_start: 0.6531 (p0) cc_final: 0.6233 (t0) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.1289 time to fit residues: 86.3966 Evaluate side-chains 211 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN B 244 ASN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 244 ASN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 HIS E 464 ASN ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114697 restraints weight = 26103.791| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.69 r_work: 0.3402 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17422 Z= 0.195 Angle : 0.718 7.871 23663 Z= 0.382 Chirality : 0.046 0.203 2642 Planarity : 0.005 0.061 3008 Dihedral : 5.150 26.826 2297 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.94 % Allowed : 6.46 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.84 (0.18), residues: 2102 helix: 1.58 (0.26), residues: 341 sheet: 1.03 (0.21), residues: 564 loop : 0.10 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 262a TYR 0.023 0.002 TYR A 168 PHE 0.022 0.003 PHE B 118 TRP 0.023 0.002 TRP E 84 HIS 0.015 0.002 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (17371) covalent geometry : angle 0.69509 / 0.38 (23534) SS BOND : bond 0.00413 / 0.26 ( 24) SS BOND : angle 2.04991 / 1.33 ( 48) hydrogen bonds : bond 0.04995 / 3.38 ( 672) hydrogen bonds : angle 6.08389 / 4.31 ( 1899) link_BETA1-4 : bond 0.00826 / 0.46 ( 9) link_BETA1-4 : angle 2.63742 / 1.77 ( 27) link_BETA1-6 : bond 0.00104 / 0.05 ( 3) link_BETA1-6 : angle 1.51111 / 0.89 ( 9) link_NAG-ASN : bond 0.00658 / 0.40 ( 15) link_NAG-ASN : angle 3.04570 / 2.11 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 249 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7917 (ptmm) REVERT: A 389 ASN cc_start: 0.8465 (t0) cc_final: 0.8242 (t0) REVERT: A 460 LYS cc_start: 0.8145 (pttt) cc_final: 0.7534 (ptmm) REVERT: H 6 GLU cc_start: 0.5471 (mp0) cc_final: 0.4596 (mp0) REVERT: H 108 MET cc_start: 0.6390 (tpt) cc_final: 0.6031 (tpt) REVERT: B 92 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.7324 (p0) REVERT: B 363 TYR cc_start: 0.5881 (p90) cc_final: 0.5528 (p90) REVERT: B 460 LYS cc_start: 0.8273 (pttt) cc_final: 0.7679 (ptmm) REVERT: B 491 TYR cc_start: 0.7311 (m-80) cc_final: 0.7016 (m-80) REVERT: C 78 PHE cc_start: 0.5813 (m-80) cc_final: 0.5605 (m-80) REVERT: E 474 ASP cc_start: 0.6457 (p0) cc_final: 0.6222 (t0) outliers start: 36 outliers final: 24 residues processed: 275 average time/residue: 0.1180 time to fit residues: 49.8696 Evaluate side-chains 227 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 146 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 189 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 117 HIS ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS E 92 ASN E 117 HIS E 344 GLN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.143067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111707 restraints weight = 26424.663| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.67 r_work: 0.3361 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17422 Z= 0.192 Angle : 0.651 10.032 23663 Z= 0.344 Chirality : 0.045 0.185 2642 Planarity : 0.004 0.051 3008 Dihedral : 4.973 26.521 2297 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.80 % Allowed : 8.29 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.18), residues: 2102 helix: 1.71 (0.27), residues: 345 sheet: 0.72 (0.21), residues: 594 loop : -0.13 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 81 TYR 0.025 0.002 TYR E 486 PHE 0.020 0.002 PHE B 439 TRP 0.022 0.002 TRP E 84 HIS 0.016 0.002 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (17371) covalent geometry : angle 0.63025 / 0.34 (23534) SS BOND : bond 0.00583 / 0.35 ( 24) SS BOND : angle 2.10493 / 1.36 ( 48) hydrogen bonds : bond 0.04447 / 3.02 ( 672) hydrogen bonds : angle 5.68677 / 4.03 ( 1899) link_BETA1-4 : bond 0.00977 / 0.55 ( 9) link_BETA1-4 : angle 1.90529 / 1.23 ( 27) link_BETA1-6 : bond 0.00117 / 0.06 ( 3) link_BETA1-6 : angle 1.51562 / 0.96 ( 9) link_NAG-ASN : bond 0.00432 / 0.26 ( 15) link_NAG-ASN : angle 2.79504 / 1.93 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 313 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8158 (ptmm) REVERT: A 354 HIS cc_start: 0.7176 (t70) cc_final: 0.6741 (t-170) REVERT: A 389 ASN cc_start: 0.8509 (t0) cc_final: 0.8297 (t0) REVERT: A 431 MET cc_start: 0.8377 (mtp) cc_final: 0.8016 (mtp) REVERT: A 460 LYS cc_start: 0.8126 (pttt) cc_final: 0.7677 (ptmt) REVERT: A 491 TYR cc_start: 0.7459 (m-80) cc_final: 0.6963 (m-80) REVERT: H 108 MET cc_start: 0.6291 (tpt) cc_final: 0.5984 (tpt) REVERT: L 24 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.6808 (ttp80) REVERT: B 92 ASN cc_start: 0.7504 (t0) cc_final: 0.7204 (p0) REVERT: B 363 TYR cc_start: 0.5929 (p90) cc_final: 0.5500 (p90) REVERT: B 460 LYS cc_start: 0.8221 (pttt) cc_final: 0.7681 (ptmt) REVERT: C 6 GLU cc_start: 0.5836 (mp0) cc_final: 0.5499 (mp0) REVERT: C 78 PHE cc_start: 0.5884 (m-80) cc_final: 0.5627 (m-80) REVERT: E 452 ARG cc_start: 0.6036 (ttp80) cc_final: 0.5560 (ptm-80) REVERT: E 491 TYR cc_start: 0.7295 (m-80) cc_final: 0.7067 (m-80) REVERT: F 6 GLU cc_start: 0.5211 (mp0) cc_final: 0.4906 (mp0) REVERT: G 24 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.7101 (ttm-80) REVERT: G 34 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7989 (m-40) outliers start: 52 outliers final: 32 residues processed: 258 average time/residue: 0.1072 time to fit residues: 43.2551 Evaluate side-chains 239 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 310 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain G residue 34 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 15 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 18 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS A 471 HIS H 39 GLN H 58 ASN L 38 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN D 38 GLN E 92 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN G 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.142597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111610 restraints weight = 26139.321| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.57 r_work: 0.3368 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17422 Z= 0.153 Angle : 0.611 10.288 23663 Z= 0.319 Chirality : 0.044 0.198 2642 Planarity : 0.004 0.054 3008 Dihedral : 4.794 25.089 2297 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.37 % Allowed : 9.21 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.56 (0.18), residues: 2102 helix: 1.81 (0.27), residues: 345 sheet: 0.74 (0.21), residues: 586 loop : -0.22 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 262a TYR 0.022 0.002 TYR B 486 PHE 0.017 0.002 PHE E 467 TRP 0.019 0.001 TRP E 84 HIS 0.011 0.002 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (17371) covalent geometry : angle 0.59117 / 0.31 (23534) SS BOND : bond 0.00550 / 0.32 ( 24) SS BOND : angle 1.94776 / 1.26 ( 48) hydrogen bonds : bond 0.04096 / 2.75 ( 672) hydrogen bonds : angle 5.45311 / 3.86 ( 1899) link_BETA1-4 : bond 0.00800 / 0.45 ( 9) link_BETA1-4 : angle 1.75966 / 1.17 ( 27) link_BETA1-6 : bond 0.00219 / 0.11 ( 3) link_BETA1-6 : angle 1.54169 / 0.97 ( 9) link_NAG-ASN : bond 0.00402 / 0.25 ( 15) link_NAG-ASN : angle 2.61547 / 1.83 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 HIS cc_start: 0.7025 (t70) cc_final: 0.6787 (t-170) REVERT: A 389 ASN cc_start: 0.8519 (t0) cc_final: 0.8285 (t0) REVERT: A 460 LYS cc_start: 0.8262 (pttt) cc_final: 0.7798 (ptmt) REVERT: A 491 TYR cc_start: 0.7328 (m-80) cc_final: 0.6881 (m-80) REVERT: H 89 VAL cc_start: 0.6938 (t) cc_final: 0.6437 (t) REVERT: H 108 MET cc_start: 0.6296 (tpt) cc_final: 0.5975 (tpt) REVERT: L 24 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.6907 (ttp80) REVERT: B 355 HIS cc_start: 0.7199 (m90) cc_final: 0.6992 (m-70) REVERT: B 363 TYR cc_start: 0.5872 (p90) cc_final: 0.5474 (p90) REVERT: B 460 LYS cc_start: 0.8216 (pttt) cc_final: 0.7705 (ptmt) REVERT: C 53 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7384 (p) REVERT: C 78 PHE cc_start: 0.6109 (m-80) cc_final: 0.5804 (m-80) REVERT: E 413 MET cc_start: 0.8625 (mtp) cc_final: 0.8414 (ttm) REVERT: E 452 ARG cc_start: 0.6057 (ttp80) cc_final: 0.5514 (ptm-80) REVERT: E 491 TYR cc_start: 0.7163 (m-80) cc_final: 0.6962 (m-80) REVERT: G 24 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7128 (ttm-80) outliers start: 44 outliers final: 28 residues processed: 262 average time/residue: 0.1364 time to fit residues: 54.9613 Evaluate side-chains 241 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN E 92 ASN E 355 HIS E 471 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.146076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114955 restraints weight = 25685.421| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.66 r_work: 0.3364 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17422 Z= 0.133 Angle : 0.586 9.179 23663 Z= 0.304 Chirality : 0.043 0.273 2642 Planarity : 0.004 0.052 3008 Dihedral : 4.647 24.452 2297 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.15 % Allowed : 10.07 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.62 (0.18), residues: 2102 helix: 1.92 (0.27), residues: 345 sheet: 0.93 (0.22), residues: 564 loop : -0.27 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 81 TYR 0.022 0.001 TYR E 486 PHE 0.019 0.002 PHE E 467 TRP 0.016 0.001 TRP E 84 HIS 0.007 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (17371) covalent geometry : angle 0.56957 / 0.30 (23534) SS BOND : bond 0.00458 / 0.26 ( 24) SS BOND : angle 1.66970 / 1.09 ( 48) hydrogen bonds : bond 0.03894 / 2.61 ( 672) hydrogen bonds : angle 5.31800 / 3.78 ( 1899) link_BETA1-4 : bond 0.00742 / 0.42 ( 9) link_BETA1-4 : angle 1.65980 / 1.11 ( 27) link_BETA1-6 : bond 0.00104 / 0.05 ( 3) link_BETA1-6 : angle 1.55585 / 0.98 ( 9) link_NAG-ASN : bond 0.00358 / 0.20 ( 15) link_NAG-ASN : angle 2.44720 / 1.74 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.8839 (mtm) cc_final: 0.8477 (mtm) REVERT: A 389 ASN cc_start: 0.8473 (t0) cc_final: 0.8054 (t0) REVERT: A 413 MET cc_start: 0.8682 (mtp) cc_final: 0.8388 (ttm) REVERT: A 460 LYS cc_start: 0.8141 (pttt) cc_final: 0.7629 (ptmt) REVERT: A 491 TYR cc_start: 0.7309 (m-80) cc_final: 0.6856 (m-80) REVERT: H 58 ASN cc_start: 0.8279 (m-40) cc_final: 0.7748 (m110) REVERT: H 89 VAL cc_start: 0.6899 (t) cc_final: 0.6425 (t) REVERT: H 108 MET cc_start: 0.6041 (tpt) cc_final: 0.5716 (tpt) REVERT: B 363 TYR cc_start: 0.6126 (p90) cc_final: 0.5586 (p90) REVERT: B 460 LYS cc_start: 0.8127 (pttt) cc_final: 0.7598 (ptmt) REVERT: C 53 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7329 (p) REVERT: C 78 PHE cc_start: 0.6110 (m-80) cc_final: 0.5666 (m-80) REVERT: E 310 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8363 (mtpt) REVERT: E 491 TYR cc_start: 0.6987 (m-80) cc_final: 0.6756 (m-80) REVERT: G 24 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7098 (ttm-80) outliers start: 40 outliers final: 25 residues processed: 252 average time/residue: 0.1375 time to fit residues: 53.0760 Evaluate side-chains 235 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 310 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 355 HIS A 382 ASN H 39 GLN E 92 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111362 restraints weight = 25822.809| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.62 r_work: 0.3322 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17422 Z= 0.186 Angle : 0.620 9.857 23663 Z= 0.321 Chirality : 0.045 0.230 2642 Planarity : 0.004 0.056 3008 Dihedral : 4.716 26.448 2297 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.58 % Allowed : 9.64 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.49 (0.18), residues: 2102 helix: 1.87 (0.26), residues: 345 sheet: 0.84 (0.22), residues: 564 loop : -0.38 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 452 TYR 0.022 0.002 TYR E 486 PHE 0.028 0.002 PHE A 118 TRP 0.020 0.001 TRP E 84 HIS 0.006 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (17371) covalent geometry : angle 0.60422 / 0.32 (23534) SS BOND : bond 0.00483 / 0.32 ( 24) SS BOND : angle 1.57080 / 1.04 ( 48) hydrogen bonds : bond 0.04048 / 2.72 ( 672) hydrogen bonds : angle 5.33986 / 3.78 ( 1899) link_BETA1-4 : bond 0.00791 / 0.44 ( 9) link_BETA1-4 : angle 1.67957 / 1.14 ( 27) link_BETA1-6 : bond 0.00394 / 0.20 ( 3) link_BETA1-6 : angle 1.62354 / 1.03 ( 9) link_NAG-ASN : bond 0.00436 / 0.29 ( 15) link_NAG-ASN : angle 2.50481 / 1.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 239 MET cc_start: 0.8878 (mtm) cc_final: 0.8507 (mtm) REVERT: A 389 ASN cc_start: 0.8431 (t0) cc_final: 0.8088 (t0) REVERT: A 413 MET cc_start: 0.8666 (mtp) cc_final: 0.8156 (ttm) REVERT: A 454 GLN cc_start: 0.8004 (mt0) cc_final: 0.7578 (tt0) REVERT: A 460 LYS cc_start: 0.8190 (pttt) cc_final: 0.7689 (ptmt) REVERT: A 491 TYR cc_start: 0.7269 (m-80) cc_final: 0.6787 (m-80) REVERT: H 58 ASN cc_start: 0.8455 (m-40) cc_final: 0.7918 (m110) REVERT: H 108 MET cc_start: 0.6110 (tpt) cc_final: 0.5788 (tpt) REVERT: B 357 ASN cc_start: 0.6142 (p0) cc_final: 0.5763 (t0) REVERT: B 363 TYR cc_start: 0.5715 (p90) cc_final: 0.5269 (p90) REVERT: B 460 LYS cc_start: 0.8079 (pttt) cc_final: 0.7548 (ptmt) REVERT: C 53 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7376 (p) REVERT: C 78 PHE cc_start: 0.6260 (m-80) cc_final: 0.5727 (m-80) REVERT: E 310 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8487 (mtpt) REVERT: E 413 MET cc_start: 0.8559 (mtp) cc_final: 0.8242 (ttm) REVERT: E 452 ARG cc_start: 0.6043 (ttp-110) cc_final: 0.5688 (ttm110) REVERT: E 491 TYR cc_start: 0.7053 (m-80) cc_final: 0.6815 (m-80) REVERT: G 24 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7056 (ttp80) outliers start: 48 outliers final: 34 residues processed: 252 average time/residue: 0.1403 time to fit residues: 53.9496 Evaluate side-chains 237 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 310 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 194 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 chunk 164 optimal weight: 0.0030 chunk 104 optimal weight: 5.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN H 39 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** E 355 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 = 0.3885 r_free = 0.3885 target = 0.143008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111875 restraints weight = 25545.131| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.61 r_work: 0.3351 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17422 Z= 0.134 Angle : 0.580 9.969 23663 Z= 0.298 Chirality : 0.043 0.225 2642 Planarity : 0.004 0.055 3008 Dihedral : 4.566 25.569 2297 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.94 % Allowed : 11.04 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.18), residues: 2102 helix: 1.97 (0.26), residues: 345 sheet: 0.94 (0.22), residues: 561 loop : -0.43 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 81 TYR 0.022 0.001 TYR B 486 PHE 0.030 0.002 PHE A 118 TRP 0.014 0.001 TRP B 84 HIS 0.004 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (17371) covalent geometry : angle 0.56513 / 0.29 (23534) SS BOND : bond 0.00446 / 0.25 ( 24) SS BOND : angle 1.63385 / 1.04 ( 48) hydrogen bonds : bond 0.03806 / 2.55 ( 672) hydrogen bonds : angle 5.27212 / 3.75 ( 1899) link_BETA1-4 : bond 0.00699 / 0.40 ( 9) link_BETA1-4 : angle 1.54943 / 1.05 ( 27) link_BETA1-6 : bond 0.00247 / 0.12 ( 3) link_BETA1-6 : angle 1.56147 / 0.99 ( 9) link_NAG-ASN : bond 0.00356 / 0.25 ( 15) link_NAG-ASN : angle 2.29082 / 1.61 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8894 (mtm) cc_final: 0.8517 (mtm) REVERT: A 389 ASN cc_start: 0.8483 (t0) cc_final: 0.8130 (t0) REVERT: A 413 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8014 (ttm) REVERT: A 454 GLN cc_start: 0.8077 (mt0) cc_final: 0.7637 (tt0) REVERT: A 460 LYS cc_start: 0.8170 (pttt) cc_final: 0.7633 (ptmt) REVERT: A 491 TYR cc_start: 0.7218 (m-80) cc_final: 0.6749 (m-80) REVERT: H 58 ASN cc_start: 0.8379 (m-40) cc_final: 0.7844 (m110) REVERT: H 108 MET cc_start: 0.6252 (tpt) cc_final: 0.5911 (tpt) REVERT: B 357 ASN cc_start: 0.6198 (p0) cc_final: 0.5899 (t0) REVERT: B 363 TYR cc_start: 0.5750 (p90) cc_final: 0.5301 (p90) REVERT: B 382 ASN cc_start: 0.8850 (m-40) cc_final: 0.8570 (m-40) REVERT: B 460 LYS cc_start: 0.8040 (pttt) cc_final: 0.7530 (ptmt) REVERT: C 53 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7417 (p) REVERT: C 78 PHE cc_start: 0.6423 (m-80) cc_final: 0.5856 (m-80) REVERT: E 310 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8436 (mtpt) REVERT: E 413 MET cc_start: 0.8543 (mtp) cc_final: 0.8312 (ttm) REVERT: E 452 ARG cc_start: 0.5934 (ttp-110) cc_final: 0.5696 (ttm110) REVERT: E 491 TYR cc_start: 0.6994 (m-80) cc_final: 0.6754 (m-80) REVERT: G 24 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7048 (ttp80) outliers start: 36 outliers final: 27 residues processed: 239 average time/residue: 0.1236 time to fit residues: 45.4091 Evaluate side-chains 237 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 310 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 20 optimal weight: 1.9990 chunk 152 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 146 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.139952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108928 restraints weight = 26019.970| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.61 r_work: 0.3323 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17422 Z= 0.185 Angle : 0.620 10.025 23663 Z= 0.318 Chirality : 0.045 0.219 2642 Planarity : 0.004 0.055 3008 Dihedral : 4.662 27.843 2297 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.21 % Allowed : 10.82 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.38 (0.18), residues: 2102 helix: 1.86 (0.26), residues: 345 sheet: 0.86 (0.22), residues: 561 loop : -0.53 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 81 TYR 0.023 0.002 TYR B 486 PHE 0.035 0.002 PHE A 118 TRP 0.018 0.001 TRP E 84 HIS 0.005 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (17371) covalent geometry : angle 0.60464 / 0.31 (23534) SS BOND : bond 0.00456 / 0.28 ( 24) SS BOND : angle 1.76812 / 1.14 ( 48) hydrogen bonds : bond 0.03983 / 2.67 ( 672) hydrogen bonds : angle 5.30917 / 3.77 ( 1899) link_BETA1-4 : bond 0.00768 / 0.43 ( 9) link_BETA1-4 : angle 1.59514 / 1.09 ( 27) link_BETA1-6 : bond 0.00395 / 0.20 ( 3) link_BETA1-6 : angle 1.62221 / 1.03 ( 9) link_NAG-ASN : bond 0.00534 / 0.32 ( 15) link_NAG-ASN : angle 2.41354 / 1.70 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7654 (p0) REVERT: A 239 MET cc_start: 0.8893 (mtm) cc_final: 0.8502 (mtm) REVERT: A 354 HIS cc_start: 0.7431 (t-90) cc_final: 0.7085 (t-170) REVERT: A 389 ASN cc_start: 0.8488 (t0) cc_final: 0.8111 (t0) REVERT: A 413 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7977 (ttm) REVERT: A 454 GLN cc_start: 0.8028 (mt0) cc_final: 0.7633 (tt0) REVERT: A 460 LYS cc_start: 0.8010 (pttt) cc_final: 0.7457 (ptmt) REVERT: A 491 TYR cc_start: 0.7309 (m-80) cc_final: 0.6579 (m-80) REVERT: H 58 ASN cc_start: 0.8449 (m-40) cc_final: 0.7929 (m110) REVERT: H 108 MET cc_start: 0.6211 (tpt) cc_final: 0.5885 (tpt) REVERT: L 83 PHE cc_start: 0.7739 (m-80) cc_final: 0.7537 (m-80) REVERT: B 357 ASN cc_start: 0.6192 (p0) cc_final: 0.5922 (t0) REVERT: B 363 TYR cc_start: 0.5728 (p90) cc_final: 0.5372 (p90) REVERT: B 382 ASN cc_start: 0.8840 (m-40) cc_final: 0.8580 (m110) REVERT: B 413 MET cc_start: 0.8651 (ttp) cc_final: 0.8382 (ttm) REVERT: B 460 LYS cc_start: 0.8010 (pttt) cc_final: 0.7503 (ptmt) REVERT: C 53 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7354 (p) REVERT: C 78 PHE cc_start: 0.6450 (m-80) cc_final: 0.5868 (m-80) REVERT: E 310 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8522 (mtpt) REVERT: E 413 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8256 (ttm) REVERT: E 452 ARG cc_start: 0.5935 (ttp-110) cc_final: 0.5517 (ttm110) REVERT: E 491 TYR cc_start: 0.7074 (m-80) cc_final: 0.6796 (m-80) REVERT: G 24 ARG cc_start: 0.7710 (ttm-80) cc_final: 0.7052 (ttp80) outliers start: 41 outliers final: 30 residues processed: 239 average time/residue: 0.1236 time to fit residues: 45.3857 Evaluate side-chains 238 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 310 LYS Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 101 optimal weight: 0.0050 chunk 168 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.143126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111919 restraints weight = 25601.607| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.63 r_work: 0.3352 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17422 Z= 0.125 Angle : 0.579 9.883 23663 Z= 0.297 Chirality : 0.043 0.231 2642 Planarity : 0.004 0.055 3008 Dihedral : 4.522 26.369 2297 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.72 % Allowed : 11.25 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.18), residues: 2102 helix: 1.86 (0.26), residues: 345 sheet: 0.95 (0.22), residues: 561 loop : -0.48 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 81 TYR 0.023 0.001 TYR B 486 PHE 0.030 0.002 PHE A 118 TRP 0.013 0.001 TRP B 84 HIS 0.004 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (17371) covalent geometry : angle 0.56323 / 0.29 (23534) SS BOND : bond 0.00390 / 0.23 ( 24) SS BOND : angle 1.87881 / 1.16 ( 48) hydrogen bonds : bond 0.03749 / 2.51 ( 672) hydrogen bonds : angle 5.25349 / 3.73 ( 1899) link_BETA1-4 : bond 0.00700 / 0.41 ( 9) link_BETA1-4 : angle 1.47477 / 1.00 ( 27) link_BETA1-6 : bond 0.00243 / 0.12 ( 3) link_BETA1-6 : angle 1.58905 / 1.01 ( 9) link_NAG-ASN : bond 0.00467 / 0.28 ( 15) link_NAG-ASN : angle 2.23098 / 1.57 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8923 (mtm) cc_final: 0.8542 (mtm) REVERT: A 389 ASN cc_start: 0.8431 (t0) cc_final: 0.8085 (t0) REVERT: A 413 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7933 (ttm) REVERT: A 454 GLN cc_start: 0.7993 (mt0) cc_final: 0.7677 (tt0) REVERT: A 459 VAL cc_start: 0.6882 (m) cc_final: 0.6641 (m) REVERT: A 460 LYS cc_start: 0.8025 (pttt) cc_final: 0.7389 (ptmt) REVERT: A 491 TYR cc_start: 0.7203 (m-80) cc_final: 0.6747 (m-80) REVERT: H 58 ASN cc_start: 0.8408 (m-40) cc_final: 0.7873 (m110) REVERT: H 108 MET cc_start: 0.6267 (tpt) cc_final: 0.5948 (tpt) REVERT: L 83 PHE cc_start: 0.7820 (m-80) cc_final: 0.7575 (m-80) REVERT: B 357 ASN cc_start: 0.6239 (p0) cc_final: 0.6023 (t0) REVERT: B 363 TYR cc_start: 0.5909 (p90) cc_final: 0.5509 (p90) REVERT: B 382 ASN cc_start: 0.8810 (m-40) cc_final: 0.8557 (m110) REVERT: B 460 LYS cc_start: 0.8056 (pttt) cc_final: 0.7503 (ptmt) REVERT: C 53 THR cc_start: 0.7936 (OUTLIER) cc_final: 0.7389 (p) REVERT: C 78 PHE cc_start: 0.6420 (m-80) cc_final: 0.5850 (m-80) REVERT: E 17 TYR cc_start: 0.7961 (p90) cc_final: 0.7707 (p90) REVERT: E 310 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8394 (mtpt) REVERT: E 452 ARG cc_start: 0.5930 (ttp-110) cc_final: 0.5681 (ttm110) REVERT: E 491 TYR cc_start: 0.6993 (m-80) cc_final: 0.6741 (m-80) REVERT: G 24 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7057 (ttp80) outliers start: 32 outliers final: 22 residues processed: 236 average time/residue: 0.1208 time to fit residues: 43.7431 Evaluate side-chains 232 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 310 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.141743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110826 restraints weight = 25549.648| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.59 r_work: 0.3351 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17422 Z= 0.151 Angle : 0.769 59.196 23663 Z= 0.436 Chirality : 0.044 0.265 2642 Planarity : 0.004 0.055 3008 Dihedral : 4.514 26.263 2297 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.62 % Allowed : 11.47 % Favored : 86.91 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.57 % 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 (0.18), residues: 2102 helix: 1.86 (0.26), residues: 345 sheet: 0.96 (0.22), residues: 561 loop : -0.48 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 81 TYR 0.022 0.001 TYR B 486 PHE 0.031 0.002 PHE A 118 TRP 0.013 0.001 TRP B 84 HIS 0.004 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (17371) covalent geometry : angle 0.75417 / 0.43 (23534) SS BOND : bond 0.00546 / 0.35 ( 24) SS BOND : angle 2.28850 / 1.38 ( 48) hydrogen bonds : bond 0.03760 / 2.52 ( 672) hydrogen bonds : angle 5.25158 / 3.72 ( 1899) link_BETA1-4 : bond 0.00663 / 0.37 ( 9) link_BETA1-4 : angle 1.47924 / 1.01 ( 27) link_BETA1-6 : bond 0.00283 / 0.14 ( 3) link_BETA1-6 : angle 1.62052 / 1.02 ( 9) link_NAG-ASN : bond 0.00558 / 0.32 ( 15) link_NAG-ASN : angle 2.42589 / 1.74 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8922 (mtm) cc_final: 0.8543 (mtm) REVERT: A 389 ASN cc_start: 0.8427 (t0) cc_final: 0.8075 (t0) REVERT: A 454 GLN cc_start: 0.7982 (mt0) cc_final: 0.7661 (tt0) REVERT: A 459 VAL cc_start: 0.6878 (m) cc_final: 0.6626 (m) REVERT: A 460 LYS cc_start: 0.8007 (pttt) cc_final: 0.7369 (ptmt) REVERT: A 491 TYR cc_start: 0.7211 (m-80) cc_final: 0.6745 (m-80) REVERT: H 58 ASN cc_start: 0.8383 (m-40) cc_final: 0.7852 (m110) REVERT: H 108 MET cc_start: 0.6247 (tpt) cc_final: 0.5928 (tpt) REVERT: L 83 PHE cc_start: 0.7809 (m-80) cc_final: 0.7560 (m-80) REVERT: B 357 ASN cc_start: 0.6233 (p0) cc_final: 0.6016 (t0) REVERT: B 363 TYR cc_start: 0.5909 (p90) cc_final: 0.5507 (p90) REVERT: B 382 ASN cc_start: 0.8799 (m-40) cc_final: 0.8547 (m110) REVERT: B 413 MET cc_start: 0.8669 (ttp) cc_final: 0.8423 (ttm) REVERT: B 460 LYS cc_start: 0.8038 (pttt) cc_final: 0.7485 (ptmt) REVERT: C 53 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7389 (p) REVERT: C 78 PHE cc_start: 0.6424 (m-80) cc_final: 0.5851 (m-80) REVERT: E 17 TYR cc_start: 0.7955 (p90) cc_final: 0.7699 (p90) REVERT: E 310 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8393 (mtpt) REVERT: E 452 ARG cc_start: 0.5933 (ttp-110) cc_final: 0.5675 (ttm110) REVERT: E 491 TYR cc_start: 0.6994 (m-80) cc_final: 0.6736 (m-80) REVERT: G 24 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7050 (ttp80) outliers start: 30 outliers final: 26 residues processed: 227 average time/residue: 0.1126 time to fit residues: 39.3790 Evaluate side-chains 232 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 310 LYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain G residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 173 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 8 optimal weight: 0.0670 chunk 162 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.141655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110853 restraints weight = 25674.355| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.58 r_work: 0.3351 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17422 Z= 0.152 Angle : 0.769 59.196 23663 Z= 0.436 Chirality : 0.044 0.265 2642 Planarity : 0.004 0.055 3008 Dihedral : 4.514 26.263 2297 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.51 % Allowed : 11.63 % Favored : 86.86 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.57 % 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 (0.18), residues: 2102 helix: 1.86 (0.26), residues: 345 sheet: 0.96 (0.22), residues: 561 loop : -0.48 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 81 TYR 0.022 0.001 TYR B 486 PHE 0.031 0.002 PHE A 118 TRP 0.013 0.001 TRP B 84 HIS 0.004 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (17371) covalent geometry : angle 0.75417 / 0.43 (23534) SS BOND : bond 0.00855 / 0.47 ( 24) SS BOND : angle 2.32722 / 1.45 ( 48) hydrogen bonds : bond 0.03760 / 2.52 ( 672) hydrogen bonds : angle 5.25158 / 3.72 ( 1899) link_BETA1-4 : bond 0.00663 / 0.37 ( 9) link_BETA1-4 : angle 1.47924 / 1.01 ( 27) link_BETA1-6 : bond 0.00283 / 0.14 ( 3) link_BETA1-6 : angle 1.62052 / 1.02 ( 9) link_NAG-ASN : bond 0.00558 / 0.32 ( 15) link_NAG-ASN : angle 2.42589 / 1.74 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4611.70 seconds wall clock time: 79 minutes 53.00 seconds (4793.00 seconds total)