Starting phenix.real_space_refine on Sun May 18 15:11:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp6_41468/05_2025/8tp6_41468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp6_41468/05_2025/8tp6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tp6_41468/05_2025/8tp6_41468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp6_41468/05_2025/8tp6_41468.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp6_41468/05_2025/8tp6_41468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp6_41468/05_2025/8tp6_41468.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.46, per 1000 atoms: 0.67 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: 4.65 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.84 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: 7.00 Time building geometry restraints manager: 5.29 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 - 21.06: 10379 21.06 - 42.11: 229 42.11 - 63.17: 60 63.17 - 84.22: 30 84.22 - 105.28: 21 Dihedral angle restraints: 10719 sinusoidal: 4638 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 10716 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 493 or resid 501 throu \ gh 503)) selection = (chain 'B' and (resid 11 through 324 or resid 335 through 493 or resid 501 throu \ gh 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 42.760 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 : 11.866 105.278 6773 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (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 TRP 0.033 0.008 TRP L 35 HIS 0.011 0.003 HIS B 354 PHE 0.052 0.008 PHE E 118 TYR 0.068 0.010 TYR E 448 ARG 0.006 0.001 ARG B 456 Details of bonding type rmsd link_NAG-ASN : bond 0.08060 ( 15) link_NAG-ASN : angle 2.87410 ( 45) link_BETA1-4 : bond 0.07358 ( 9) link_BETA1-4 : angle 5.01980 ( 27) hydrogen bonds : bond 0.13767 ( 672) hydrogen bonds : angle 7.69596 ( 1899) link_BETA1-6 : bond 0.04691 ( 3) link_BETA1-6 : angle 3.04491 ( 9) SS BOND : bond 0.00712 ( 24) SS BOND : angle 2.34758 ( 48) covalent geometry : bond 0.02101 (17371) covalent geometry : angle 1.77456 (23534) *********************** 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 : 1.999 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: 0.3147 time to fit residues: 208.6612 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 : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 176 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN E 244 ASN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.147497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116807 restraints weight = 26032.387| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.68 r_work: 0.3436 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17422 Z= 0.165 Angle : 0.707 8.320 23663 Z= 0.370 Chirality : 0.046 0.208 2642 Planarity : 0.005 0.065 3008 Dihedral : 8.348 69.078 2846 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.56 % Allowed : 6.79 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2102 helix: 1.60 (0.26), residues: 344 sheet: 1.12 (0.22), residues: 558 loop : 0.10 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 84 HIS 0.014 0.002 HIS B 354 PHE 0.017 0.002 PHE B 118 TYR 0.024 0.002 TYR A 168 ARG 0.006 0.001 ARG B 262a Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 15) link_NAG-ASN : angle 3.05525 ( 45) link_BETA1-4 : bond 0.00793 ( 9) link_BETA1-4 : angle 3.27238 ( 27) hydrogen bonds : bond 0.04788 ( 672) hydrogen bonds : angle 6.09947 ( 1899) link_BETA1-6 : bond 0.00031 ( 3) link_BETA1-6 : angle 1.61127 ( 9) SS BOND : bond 0.01157 ( 24) SS BOND : angle 1.76899 ( 48) covalent geometry : bond 0.00355 (17371) covalent geometry : angle 0.68185 (23534) *********************** 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 294 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 HIS cc_start: 0.7084 (t-90) cc_final: 0.6849 (t70) REVERT: A 460 LYS cc_start: 0.8117 (pttt) cc_final: 0.7577 (ptmm) REVERT: H 6 GLU cc_start: 0.5437 (mp0) cc_final: 0.4634 (mp0) REVERT: L 21 ILE cc_start: 0.8935 (mt) cc_final: 0.8722 (mp) REVERT: B 92 ASN cc_start: 0.7476 (t0) cc_final: 0.7246 (p0) REVERT: B 348 ASP cc_start: 0.8055 (m-30) cc_final: 0.7793 (m-30) REVERT: B 363 TYR cc_start: 0.5821 (p90) cc_final: 0.5366 (p90) REVERT: B 460 LYS cc_start: 0.8240 (pttt) cc_final: 0.7567 (ptmm) REVERT: B 491 TYR cc_start: 0.7254 (m-80) cc_final: 0.6995 (m-80) REVERT: C 6 GLU cc_start: 0.5807 (mp0) cc_final: 0.5438 (mp0) REVERT: C 78 PHE cc_start: 0.5870 (m-80) cc_final: 0.5624 (m-80) REVERT: E 474 ASP cc_start: 0.6437 (p0) cc_final: 0.6221 (t0) outliers start: 29 outliers final: 20 residues processed: 286 average time/residue: 0.2814 time to fit residues: 122.2145 Evaluate side-chains 228 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 1.905 ------------------------------------------------------------------------------- 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 60 SER 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 198 VAL Chi-restraints excluded: chain C residue 23 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 348 ASP Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 109 optimal weight: 3.9990 chunk 187 optimal weight: 0.0470 chunk 21 optimal weight: 3.9990 chunk 197 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 117 HIS A 244 ASN A 355 HIS ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 HIS ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 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 = 0.3895 r_free = 0.3895 target = 0.144310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112803 restraints weight = 26022.862| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.66 r_work: 0.3373 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17422 Z= 0.174 Angle : 0.646 9.590 23663 Z= 0.340 Chirality : 0.045 0.195 2642 Planarity : 0.004 0.051 3008 Dihedral : 6.584 42.185 2846 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.64 % Allowed : 8.62 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.18), residues: 2102 helix: 1.80 (0.27), residues: 345 sheet: 0.93 (0.21), residues: 574 loop : -0.13 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 84 HIS 0.011 0.002 HIS B 354 PHE 0.021 0.002 PHE A 439 TYR 0.026 0.002 TYR E 486 ARG 0.006 0.000 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 15) link_NAG-ASN : angle 2.87482 ( 45) link_BETA1-4 : bond 0.01096 ( 9) link_BETA1-4 : angle 2.56633 ( 27) hydrogen bonds : bond 0.04372 ( 672) hydrogen bonds : angle 5.60988 ( 1899) link_BETA1-6 : bond 0.00107 ( 3) link_BETA1-6 : angle 1.66559 ( 9) SS BOND : bond 0.00657 ( 24) SS BOND : angle 1.85662 ( 48) covalent geometry : bond 0.00392 (17371) covalent geometry : angle 0.62266 (23534) *********************** 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 279 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 1.701 Fit side-chains revert: symmetry clash REVERT: A 431 MET cc_start: 0.8335 (mtp) cc_final: 0.8014 (mtp) REVERT: A 460 LYS cc_start: 0.8240 (pttt) cc_final: 0.7749 (ptmt) REVERT: A 478 MET cc_start: 0.6539 (mmm) cc_final: 0.6290 (mmm) REVERT: A 491 TYR cc_start: 0.7340 (m-80) cc_final: 0.6888 (m-80) REVERT: B 92 ASN cc_start: 0.7736 (t0) cc_final: 0.7483 (p0) REVERT: B 354 HIS cc_start: 0.7426 (t70) cc_final: 0.7089 (t-170) REVERT: B 363 TYR cc_start: 0.5795 (p90) cc_final: 0.5443 (p90) REVERT: B 460 LYS cc_start: 0.8052 (pttt) cc_final: 0.7517 (ptmt) REVERT: B 467 PHE cc_start: 0.7975 (m-80) cc_final: 0.7744 (m-80) REVERT: B 491 TYR cc_start: 0.7359 (m-80) cc_final: 0.7092 (m-80) REVERT: C 78 PHE cc_start: 0.5902 (m-80) cc_final: 0.5666 (m-80) REVERT: E 460 LYS cc_start: 0.8253 (ptmt) cc_final: 0.7790 (ptmm) REVERT: E 474 ASP cc_start: 0.6413 (p0) cc_final: 0.6164 (t0) REVERT: E 491 TYR cc_start: 0.7163 (m-80) cc_final: 0.6937 (m-80) REVERT: F 6 GLU cc_start: 0.5218 (mp0) cc_final: 0.4871 (mp0) REVERT: F 78 PHE cc_start: 0.5958 (m-80) cc_final: 0.5272 (m-80) REVERT: G 24 ARG cc_start: 0.7556 (ttm-80) cc_final: 0.7116 (ttm-80) REVERT: G 34 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.8040 (m-40) outliers start: 49 outliers final: 30 residues processed: 261 average time/residue: 0.2673 time to fit residues: 107.0964 Evaluate side-chains 233 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 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 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 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 310 LYS 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 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 99 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 200 optimal weight: 0.0970 chunk 119 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 HIS H 58 ASN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.144789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113180 restraints weight = 25972.546| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.68 r_work: 0.3377 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17422 Z= 0.138 Angle : 0.603 9.802 23663 Z= 0.313 Chirality : 0.044 0.200 2642 Planarity : 0.004 0.052 3008 Dihedral : 5.849 40.398 2846 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.15 % Allowed : 9.53 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2102 helix: 1.83 (0.27), residues: 345 sheet: 0.97 (0.21), residues: 566 loop : -0.17 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 84 HIS 0.015 0.002 HIS A 354 PHE 0.016 0.002 PHE E 467 TYR 0.022 0.002 TYR B 486 ARG 0.008 0.000 ARG A 262a Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 15) link_NAG-ASN : angle 2.70390 ( 45) link_BETA1-4 : bond 0.00828 ( 9) link_BETA1-4 : angle 2.48294 ( 27) hydrogen bonds : bond 0.04029 ( 672) hydrogen bonds : angle 5.41870 ( 1899) link_BETA1-6 : bond 0.00075 ( 3) link_BETA1-6 : angle 1.71283 ( 9) SS BOND : bond 0.00489 ( 24) SS BOND : angle 1.78286 ( 48) covalent geometry : bond 0.00310 (17371) covalent geometry : angle 0.58072 (23534) *********************** 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 257 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 2.079 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8665 (ptpp) cc_final: 0.8446 (ptpt) REVERT: A 239 MET cc_start: 0.8827 (mtm) cc_final: 0.8468 (mtm) REVERT: A 354 HIS cc_start: 0.7054 (t70) cc_final: 0.6759 (t-170) REVERT: A 460 LYS cc_start: 0.8293 (pttt) cc_final: 0.7786 (ptmt) REVERT: A 491 TYR cc_start: 0.7294 (m-80) cc_final: 0.6918 (m-80) REVERT: B 92 ASN cc_start: 0.7761 (t0) cc_final: 0.7528 (p0) REVERT: B 363 TYR cc_start: 0.5910 (p90) cc_final: 0.5481 (p90) REVERT: B 413 MET cc_start: 0.8657 (mtp) cc_final: 0.8372 (ttm) REVERT: B 460 LYS cc_start: 0.8097 (pttt) cc_final: 0.7554 (ptmt) REVERT: C 53 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7350 (p) REVERT: C 78 PHE cc_start: 0.6107 (m-80) cc_final: 0.5802 (m-80) REVERT: E 262 ARG cc_start: 0.6651 (mmm160) cc_final: 0.6386 (mmm160) REVERT: E 413 MET cc_start: 0.8687 (mtp) cc_final: 0.8351 (ttm) REVERT: E 482 LYS cc_start: 0.7418 (pttp) cc_final: 0.7205 (mtmt) REVERT: E 491 TYR cc_start: 0.7016 (m-80) cc_final: 0.6793 (m-80) REVERT: G 24 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.7123 (ttm-80) outliers start: 40 outliers final: 24 residues processed: 244 average time/residue: 0.2806 time to fit residues: 103.9626 Evaluate side-chains 228 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 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 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 E residue 23 THR Chi-restraints excluded: chain E residue 35 THR 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 G residue 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 138 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 38 GLN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 F 39 GLN G 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.142931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111321 restraints weight = 26317.361| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.68 r_work: 0.3351 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3755 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= 0.167 Angle : 0.603 8.880 23663 Z= 0.313 Chirality : 0.044 0.186 2642 Planarity : 0.004 0.053 3008 Dihedral : 5.519 37.299 2846 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.48 % Allowed : 9.37 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2102 helix: 1.80 (0.27), residues: 345 sheet: 0.90 (0.22), residues: 560 loop : -0.30 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 84 HIS 0.014 0.001 HIS A 354 PHE 0.022 0.002 PHE E 467 TYR 0.021 0.002 TYR B 486 ARG 0.007 0.000 ARG E 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 15) link_NAG-ASN : angle 2.58738 ( 45) link_BETA1-4 : bond 0.00839 ( 9) link_BETA1-4 : angle 2.26219 ( 27) hydrogen bonds : bond 0.04010 ( 672) hydrogen bonds : angle 5.37542 ( 1899) link_BETA1-6 : bond 0.00288 ( 3) link_BETA1-6 : angle 1.77861 ( 9) SS BOND : bond 0.00454 ( 24) SS BOND : angle 1.76965 ( 48) covalent geometry : bond 0.00384 (17371) covalent geometry : angle 0.58285 (23534) *********************** 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 261 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8705 (ptpp) cc_final: 0.8482 (ptpt) REVERT: A 239 MET cc_start: 0.8866 (mtm) cc_final: 0.8478 (mtm) REVERT: A 460 LYS cc_start: 0.8255 (pttt) cc_final: 0.7789 (ptmt) REVERT: A 491 TYR cc_start: 0.7218 (m-80) cc_final: 0.6832 (m-80) REVERT: H 58 ASN cc_start: 0.8403 (m-40) cc_final: 0.7900 (m110) REVERT: B 363 TYR cc_start: 0.6111 (p90) cc_final: 0.5568 (p90) REVERT: B 413 MET cc_start: 0.8625 (mtp) cc_final: 0.8324 (ttm) REVERT: B 460 LYS cc_start: 0.8130 (pttt) cc_final: 0.7578 (ptmt) REVERT: B 467 PHE cc_start: 0.7929 (m-80) cc_final: 0.7724 (m-80) REVERT: C 53 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7396 (p) REVERT: C 78 PHE cc_start: 0.6066 (m-80) cc_final: 0.5620 (m-80) REVERT: E 355 HIS cc_start: 0.7072 (m90) cc_final: 0.6747 (m170) REVERT: E 413 MET cc_start: 0.8596 (mtp) cc_final: 0.8324 (ttm) REVERT: E 452 ARG cc_start: 0.6029 (ttp-110) cc_final: 0.5157 (ptm-80) REVERT: E 491 TYR cc_start: 0.7009 (m-80) cc_final: 0.6789 (m-80) REVERT: G 24 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7151 (ttm-80) outliers start: 46 outliers final: 31 residues processed: 251 average time/residue: 0.2828 time to fit residues: 107.1333 Evaluate side-chains 239 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 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 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 459 VAL 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 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 161 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 202 optimal weight: 0.1980 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** 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 = 0.3871 r_free = 0.3871 target = 0.141859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110729 restraints weight = 25935.853| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.63 r_work: 0.3333 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17422 Z= 0.171 Angle : 0.609 8.711 23663 Z= 0.315 Chirality : 0.045 0.242 2642 Planarity : 0.004 0.055 3008 Dihedral : 5.426 37.224 2846 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.48 % Allowed : 9.59 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2102 helix: 1.75 (0.26), residues: 345 sheet: 0.90 (0.22), residues: 561 loop : -0.46 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 84 HIS 0.008 0.001 HIS A 354 PHE 0.032 0.002 PHE A 118 TYR 0.023 0.002 TYR B 486 ARG 0.006 0.000 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 15) link_NAG-ASN : angle 2.55956 ( 45) link_BETA1-4 : bond 0.00776 ( 9) link_BETA1-4 : angle 2.06754 ( 27) hydrogen bonds : bond 0.03987 ( 672) hydrogen bonds : angle 5.33982 ( 1899) link_BETA1-6 : bond 0.00260 ( 3) link_BETA1-6 : angle 1.78645 ( 9) SS BOND : bond 0.00417 ( 24) SS BOND : angle 1.68381 ( 48) covalent geometry : bond 0.00395 (17371) covalent geometry : angle 0.59034 (23534) *********************** 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 266 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8863 (mtm) cc_final: 0.8487 (mtm) REVERT: A 460 LYS cc_start: 0.8185 (pttt) cc_final: 0.7663 (ptmt) REVERT: A 491 TYR cc_start: 0.7248 (m-80) cc_final: 0.6840 (m-80) REVERT: H 58 ASN cc_start: 0.8392 (m-40) cc_final: 0.7880 (m110) REVERT: B 363 TYR cc_start: 0.5854 (p90) cc_final: 0.5375 (p90) REVERT: B 413 MET cc_start: 0.8572 (mtp) cc_final: 0.8353 (ttm) REVERT: B 460 LYS cc_start: 0.8032 (pttt) cc_final: 0.7514 (ptmt) REVERT: B 467 PHE cc_start: 0.7952 (m-80) cc_final: 0.7693 (m-80) REVERT: C 53 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7395 (p) REVERT: C 78 PHE cc_start: 0.6239 (m-80) cc_final: 0.5705 (m-80) REVERT: D 24 ARG cc_start: 0.7457 (ttm-80) cc_final: 0.7134 (ttm-80) REVERT: E 310 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8543 (mtpt) REVERT: E 413 MET cc_start: 0.8400 (mtp) cc_final: 0.8119 (ttm) REVERT: E 452 ARG cc_start: 0.5879 (ttp-110) cc_final: 0.5463 (ttm110) REVERT: E 491 TYR cc_start: 0.7030 (m-80) cc_final: 0.6794 (m-80) REVERT: G 24 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.7145 (ttm-80) outliers start: 46 outliers final: 35 residues processed: 255 average time/residue: 0.2860 time to fit residues: 109.6148 Evaluate side-chains 242 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain G residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** E 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3869 r_free = 0.3869 target = 0.141811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110743 restraints weight = 25799.728| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.61 r_work: 0.3332 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17422 Z= 0.163 Angle : 0.607 10.512 23663 Z= 0.312 Chirality : 0.044 0.231 2642 Planarity : 0.004 0.055 3008 Dihedral : 5.389 37.140 2846 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.37 % Allowed : 10.02 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2102 helix: 1.84 (0.26), residues: 345 sheet: 0.91 (0.22), residues: 561 loop : -0.48 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 84 HIS 0.004 0.001 HIS B 184 PHE 0.036 0.002 PHE A 118 TYR 0.024 0.002 TYR B 486 ARG 0.007 0.000 ARG F 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 15) link_NAG-ASN : angle 2.55691 ( 45) link_BETA1-4 : bond 0.00772 ( 9) link_BETA1-4 : angle 1.90889 ( 27) hydrogen bonds : bond 0.03894 ( 672) hydrogen bonds : angle 5.29493 ( 1899) link_BETA1-6 : bond 0.00238 ( 3) link_BETA1-6 : angle 1.80874 ( 9) SS BOND : bond 0.00480 ( 24) SS BOND : angle 1.67258 ( 48) covalent geometry : bond 0.00375 (17371) covalent geometry : angle 0.58937 (23534) *********************** 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 259 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.7948 (t0) cc_final: 0.7554 (p0) REVERT: A 239 MET cc_start: 0.8870 (mtm) cc_final: 0.8467 (mtm) REVERT: A 460 LYS cc_start: 0.8121 (pttt) cc_final: 0.7596 (ptmt) REVERT: A 491 TYR cc_start: 0.7215 (m-80) cc_final: 0.6807 (m-80) REVERT: H 58 ASN cc_start: 0.8426 (m-40) cc_final: 0.7917 (m110) REVERT: L 83 PHE cc_start: 0.7836 (m-80) cc_final: 0.7579 (m-80) REVERT: B 357 ASN cc_start: 0.6058 (p0) cc_final: 0.5448 (t0) REVERT: B 363 TYR cc_start: 0.5972 (p90) cc_final: 0.5427 (p90) REVERT: B 382 ASN cc_start: 0.8882 (m-40) cc_final: 0.8592 (m110) REVERT: B 460 LYS cc_start: 0.8088 (pttt) cc_final: 0.7535 (ptmt) REVERT: C 53 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7434 (p) REVERT: C 78 PHE cc_start: 0.6415 (m-80) cc_final: 0.5829 (m-80) REVERT: E 310 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8532 (mtpt) REVERT: E 413 MET cc_start: 0.8394 (mtp) cc_final: 0.8161 (ttm) REVERT: E 452 ARG cc_start: 0.6000 (ttp-110) cc_final: 0.5753 (ttm110) REVERT: E 491 TYR cc_start: 0.7014 (m-80) cc_final: 0.6766 (m-80) REVERT: F 52 TYR cc_start: 0.8393 (m-80) cc_final: 0.8128 (m-80) REVERT: G 24 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.6983 (ttp80) outliers start: 44 outliers final: 36 residues processed: 246 average time/residue: 0.3116 time to fit residues: 117.6250 Evaluate side-chains 240 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 1.973 ------------------------------------------------------------------------------- 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 118 PHE 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 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 68 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 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 Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 169 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** E 354 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 = 0.3888 r_free = 0.3888 target = 0.143336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112200 restraints weight = 25565.997| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.62 r_work: 0.3353 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17422 Z= 0.126 Angle : 0.585 12.787 23663 Z= 0.298 Chirality : 0.044 0.240 2642 Planarity : 0.004 0.054 3008 Dihedral : 5.181 37.046 2846 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.05 % Allowed : 10.77 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2102 helix: 1.93 (0.26), residues: 344 sheet: 0.97 (0.22), residues: 561 loop : -0.46 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 84 HIS 0.004 0.001 HIS A 354 PHE 0.032 0.002 PHE A 118 TYR 0.024 0.001 TYR B 486 ARG 0.008 0.000 ARG D 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 15) link_NAG-ASN : angle 2.39107 ( 45) link_BETA1-4 : bond 0.00724 ( 9) link_BETA1-4 : angle 1.81217 ( 27) hydrogen bonds : bond 0.03731 ( 672) hydrogen bonds : angle 5.23842 ( 1899) link_BETA1-6 : bond 0.00121 ( 3) link_BETA1-6 : angle 1.77918 ( 9) SS BOND : bond 0.00509 ( 24) SS BOND : angle 2.31062 ( 48) covalent geometry : bond 0.00285 (17371) covalent geometry : angle 0.56277 (23534) *********************** 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 258 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.7920 (t0) cc_final: 0.7602 (p0) REVERT: A 239 MET cc_start: 0.8885 (mtm) cc_final: 0.8483 (mtm) REVERT: A 459 VAL cc_start: 0.6826 (m) cc_final: 0.6569 (m) REVERT: A 460 LYS cc_start: 0.7973 (pttt) cc_final: 0.7310 (ptmt) REVERT: A 485 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7827 (p) REVERT: A 491 TYR cc_start: 0.7195 (m-80) cc_final: 0.6788 (m-80) REVERT: H 58 ASN cc_start: 0.8344 (m-40) cc_final: 0.7833 (m110) REVERT: L 83 PHE cc_start: 0.7781 (m-80) cc_final: 0.7566 (m-80) REVERT: B 357 ASN cc_start: 0.6139 (p0) cc_final: 0.5833 (t0) REVERT: B 363 TYR cc_start: 0.6050 (p90) cc_final: 0.5489 (p90) REVERT: B 382 ASN cc_start: 0.8865 (m-40) cc_final: 0.8563 (m110) REVERT: B 460 LYS cc_start: 0.8024 (pttt) cc_final: 0.7453 (ptmt) REVERT: C 53 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7449 (p) REVERT: C 78 PHE cc_start: 0.6397 (m-80) cc_final: 0.5816 (m-80) REVERT: E 310 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8467 (mtpt) REVERT: E 452 ARG cc_start: 0.5964 (ttp-110) cc_final: 0.5734 (ttm110) REVERT: E 491 TYR cc_start: 0.6989 (m-80) cc_final: 0.6739 (m-80) REVERT: G 24 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.6971 (ttp80) outliers start: 38 outliers final: 25 residues processed: 246 average time/residue: 0.2821 time to fit residues: 105.9927 Evaluate side-chains 240 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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 277 CYS Chi-restraints excluded: chain A residue 413 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 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 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 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 Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 4 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 0.1980 chunk 97 optimal weight: 8.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN E 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109479 restraints weight = 25883.122| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.62 r_work: 0.3312 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17422 Z= 0.204 Angle : 0.645 12.443 23663 Z= 0.329 Chirality : 0.046 0.242 2642 Planarity : 0.005 0.056 3008 Dihedral : 5.445 40.502 2846 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.05 % Allowed : 10.66 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2102 helix: 1.80 (0.26), residues: 345 sheet: 0.62 (0.22), residues: 566 loop : -0.57 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 84 HIS 0.005 0.001 HIS B 184 PHE 0.040 0.002 PHE A 118 TYR 0.022 0.002 TYR B 486 ARG 0.009 0.001 ARG F 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 15) link_NAG-ASN : angle 2.57933 ( 45) link_BETA1-4 : bond 0.00779 ( 9) link_BETA1-4 : angle 1.85814 ( 27) hydrogen bonds : bond 0.04028 ( 672) hydrogen bonds : angle 5.36590 ( 1899) link_BETA1-6 : bond 0.00286 ( 3) link_BETA1-6 : angle 1.91378 ( 9) SS BOND : bond 0.00627 ( 24) SS BOND : angle 2.40997 ( 48) covalent geometry : bond 0.00479 (17371) covalent geometry : angle 0.62325 (23534) *********************** 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: 38 poor density : 209 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8058 (t0) cc_final: 0.7781 (p0) REVERT: A 239 MET cc_start: 0.8894 (mtm) cc_final: 0.8492 (mtm) REVERT: A 459 VAL cc_start: 0.6843 (m) cc_final: 0.6608 (m) REVERT: A 460 LYS cc_start: 0.7990 (pttt) cc_final: 0.7374 (ptmt) REVERT: A 485 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7851 (p) REVERT: A 491 TYR cc_start: 0.7305 (m-80) cc_final: 0.6873 (m-80) REVERT: L 83 PHE cc_start: 0.7721 (m-80) cc_final: 0.7483 (m-80) REVERT: B 357 ASN cc_start: 0.6211 (p0) cc_final: 0.5876 (t0) REVERT: B 363 TYR cc_start: 0.6060 (p90) cc_final: 0.5533 (p90) REVERT: B 382 ASN cc_start: 0.8873 (m-40) cc_final: 0.8588 (m110) REVERT: B 460 LYS cc_start: 0.8079 (pttt) cc_final: 0.7531 (ptmt) REVERT: C 53 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7476 (p) REVERT: C 78 PHE cc_start: 0.6431 (m-80) cc_final: 0.5809 (m-80) REVERT: E 452 ARG cc_start: 0.6030 (ttp-110) cc_final: 0.5779 (ttm110) REVERT: E 491 TYR cc_start: 0.7099 (m-80) cc_final: 0.6822 (m-80) REVERT: F 52 TYR cc_start: 0.8501 (m-80) cc_final: 0.8214 (m-80) outliers start: 38 outliers final: 31 residues processed: 236 average time/residue: 0.2916 time to fit residues: 104.9949 Evaluate side-chains 238 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 277 CYS Chi-restraints excluded: chain A residue 413 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 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 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 33 LEU 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 176 MET Chi-restraints excluded: chain E residue 455 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 F residue 107 THR Chi-restraints excluded: chain G residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 111 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 122 optimal weight: 0.0970 chunk 121 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.141107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109941 restraints weight = 25897.757| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.62 r_work: 0.3314 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 17422 Z= 0.190 Angle : 0.841 59.200 23663 Z= 0.462 Chirality : 0.045 0.233 2642 Planarity : 0.005 0.056 3008 Dihedral : 5.451 40.527 2846 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.83 % Allowed : 11.42 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2102 helix: 1.76 (0.26), residues: 345 sheet: 0.62 (0.22), residues: 566 loop : -0.57 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 84 HIS 0.004 0.001 HIS A 184 PHE 0.062 0.003 PHE A 118 TYR 0.022 0.002 TYR B 486 ARG 0.008 0.001 ARG F 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 15) link_NAG-ASN : angle 2.56976 ( 45) link_BETA1-4 : bond 0.00703 ( 9) link_BETA1-4 : angle 1.81759 ( 27) hydrogen bonds : bond 0.03963 ( 672) hydrogen bonds : angle 5.37038 ( 1899) link_BETA1-6 : bond 0.00204 ( 3) link_BETA1-6 : angle 1.91163 ( 9) SS BOND : bond 0.00686 ( 24) SS BOND : angle 4.78596 ( 48) covalent geometry : bond 0.00415 (17371) covalent geometry : angle 0.80370 (23534) ********************** 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 237 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8047 (t0) cc_final: 0.7760 (p0) REVERT: A 239 MET cc_start: 0.8884 (mtm) cc_final: 0.8479 (mtm) REVERT: A 459 VAL cc_start: 0.6842 (m) cc_final: 0.6598 (m) REVERT: A 460 LYS cc_start: 0.7985 (pttt) cc_final: 0.7370 (ptmt) REVERT: A 485 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7843 (p) REVERT: A 491 TYR cc_start: 0.7297 (m-80) cc_final: 0.6868 (m-80) REVERT: H 58 ASN cc_start: 0.8357 (m-40) cc_final: 0.7829 (t0) REVERT: L 83 PHE cc_start: 0.7718 (m-80) cc_final: 0.7477 (m-80) REVERT: B 357 ASN cc_start: 0.6235 (p0) cc_final: 0.5939 (t0) REVERT: B 363 TYR cc_start: 0.6050 (p90) cc_final: 0.5524 (p90) REVERT: B 382 ASN cc_start: 0.8868 (m-40) cc_final: 0.8581 (m110) REVERT: B 460 LYS cc_start: 0.8073 (pttt) cc_final: 0.7526 (ptmt) REVERT: C 53 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7473 (p) REVERT: C 78 PHE cc_start: 0.6417 (m-80) cc_final: 0.5801 (m-80) REVERT: E 92 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.7119 (p0) REVERT: E 452 ARG cc_start: 0.6025 (ttp-110) cc_final: 0.5771 (ttm110) REVERT: E 491 TYR cc_start: 0.7091 (m-80) cc_final: 0.6814 (m-80) REVERT: F 52 TYR cc_start: 0.8496 (m-80) cc_final: 0.8201 (m-80) outliers start: 34 outliers final: 30 residues processed: 225 average time/residue: 0.2808 time to fit residues: 95.8680 Evaluate side-chains 235 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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 118 PHE 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 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 118 PHE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 33 LEU 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 176 MET Chi-restraints excluded: chain E residue 455 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 F residue 107 THR Chi-restraints excluded: chain G residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 52 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 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 = 0.3843 r_free = 0.3843 target = 0.139428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108468 restraints weight = 25904.559| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.60 r_work: 0.3317 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.614 17422 Z= 0.644 Angle : 0.866 51.229 23663 Z= 0.462 Chirality : 0.045 0.233 2642 Planarity : 0.005 0.056 3008 Dihedral : 5.451 40.527 2846 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.72 % Allowed : 11.52 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2102 helix: 1.76 (0.26), residues: 345 sheet: 0.62 (0.22), residues: 566 loop : -0.57 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 84 HIS 0.004 0.001 HIS A 184 PHE 0.062 0.003 PHE A 118 TYR 0.022 0.002 TYR B 486 ARG 0.008 0.001 ARG F 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 15) link_NAG-ASN : angle 2.56976 ( 45) link_BETA1-4 : bond 0.00703 ( 9) link_BETA1-4 : angle 1.81759 ( 27) hydrogen bonds : bond 0.03963 ( 672) hydrogen bonds : angle 5.37038 ( 1899) link_BETA1-6 : bond 0.00204 ( 3) link_BETA1-6 : angle 1.91163 ( 9) SS BOND : bond 0.33024 ( 24) SS BOND : angle 8.97975 ( 48) covalent geometry : bond 0.00418 (17371) covalent geometry : angle 0.75652 (23534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9413.57 seconds wall clock time: 163 minutes 40.28 seconds (9820.28 seconds total)