Starting phenix.real_space_refine on Sun Aug 24 05:01:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp6_41468/08_2025/8tp6_41468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp6_41468/08_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_41468/08_2025/8tp6_41468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp6_41468/08_2025/8tp6_41468.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp6_41468/08_2025/8tp6_41468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp6_41468/08_2025/8tp6_41468.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10626 2.51 5 N 2864 2.21 5 O 3422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17008 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3806 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 19, 'TRANS': 460} Chain breaks: 1 Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "B" Number of atoms: 3806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3806 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 19, 'TRANS': 460} Chain breaks: 1 Chain: "C" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "D" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "E" Number of atoms: 3801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3801 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 19, 'TRANS': 459} Chain breaks: 1 Chain: "F" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 924 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen 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: 4.52, per 1000 atoms: 0.27 Number of scatterers: 17008 At special positions: 0 Unit cell: (121.9, 124.2, 166.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3422 8.00 N 2864 7.00 C 10626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.05 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.05 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E 466 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.05 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.02 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 477 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG P 1 " - " NAG P 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG Y 1 " - " NAG Y 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG h 1 " - " NAG h 2 " BETA1-6 " NAG K 1 " - " FUC K 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 4 " " NAG d 1 " - " FUC d 4 " NAG-ASN " NAG A 501 " - " ASN A 21 " " NAG A 502 " - " ASN A 33 " " NAG A 503 " - " ASN A 483 " " NAG B 501 " - " ASN B 21 " " NAG B 502 " - " ASN B 33 " " NAG B 503 " - " ASN B 483 " " NAG E 501 " - " ASN E 21 " " NAG E 502 " - " ASN E 33 " " NAG E 503 " - " ASN E 483 " " NAG K 1 " - " ASN A 169 " " NAG P 1 " - " ASN A 289 " " NAG U 1 " - " ASN B 169 " " NAG Y 1 " - " ASN B 289 " " NAG d 1 " - " ASN E 169 " " NAG h 1 " - " ASN E 289 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 759.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3874 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 51 sheets defined 19.6% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 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: 3.53 Time building geometry restraints manager: 2.12 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 503)) selection = (chain 'B' and (resid 11 through 324 or resid 335 through 503)) selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'U' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'Y' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.760 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.350 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.17), residues: 2102 helix: 0.52 (0.24), residues: 341 sheet: 1.20 (0.20), residues: 561 loop : 0.61 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 456 TYR 0.068 0.010 TYR E 448 PHE 0.052 0.008 PHE E 118 TRP 0.033 0.008 TRP L 35 HIS 0.011 0.003 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.02101 (17371) covalent geometry : angle 1.77456 (23534) SS BOND : bond 0.00712 ( 24) SS BOND : angle 2.34758 ( 48) hydrogen bonds : bond 0.13767 ( 672) hydrogen bonds : angle 7.69596 ( 1899) link_BETA1-4 : bond 0.07358 ( 9) link_BETA1-4 : angle 5.01980 ( 27) link_BETA1-6 : bond 0.04691 ( 3) link_BETA1-6 : angle 3.04491 ( 9) link_NAG-ASN : bond 0.08060 ( 15) link_NAG-ASN : angle 2.87410 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.665 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: 0.1464 time to fit residues: 97.4662 Evaluate side-chains 211 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN B 244 ASN ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 244 ASN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 HIS ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114764 restraints weight = 26105.798| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.69 r_work: 0.3402 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 0.062 17422 Z= 0.200 Angle : 0.725 8.027 23663 Z= 0.381 Chirality : 0.047 0.209 2642 Planarity : 0.005 0.062 3008 Dihedral : 8.437 69.271 2846 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.88 % Allowed : 6.52 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.18), residues: 2102 helix: 1.56 (0.26), residues: 342 sheet: 1.02 (0.21), residues: 564 loop : 0.08 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 24 TYR 0.023 0.002 TYR A 168 PHE 0.021 0.003 PHE B 118 TRP 0.023 0.002 TRP E 84 HIS 0.014 0.002 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00435 (17371) covalent geometry : angle 0.69844 (23534) SS BOND : bond 0.00542 ( 24) SS BOND : angle 1.93297 ( 48) hydrogen bonds : bond 0.04910 ( 672) hydrogen bonds : angle 6.08283 ( 1899) link_BETA1-4 : bond 0.01073 ( 9) link_BETA1-4 : angle 3.28220 ( 27) link_BETA1-6 : bond 0.00464 ( 3) link_BETA1-6 : angle 1.86847 ( 9) link_NAG-ASN : bond 0.00581 ( 15) link_NAG-ASN : angle 3.14720 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7921 (ptmm) REVERT: A 389 ASN cc_start: 0.8464 (t0) cc_final: 0.8240 (t0) REVERT: A 460 LYS cc_start: 0.8143 (pttt) cc_final: 0.7525 (ptmm) REVERT: A 486 TYR cc_start: 0.7085 (t80) cc_final: 0.6674 (t80) REVERT: A 491 TYR cc_start: 0.7086 (m-80) cc_final: 0.6567 (m-80) REVERT: H 6 GLU cc_start: 0.5472 (mp0) cc_final: 0.4595 (mp0) REVERT: H 108 MET cc_start: 0.6380 (tpt) cc_final: 0.6026 (tpt) REVERT: B 348 ASP cc_start: 0.8161 (m-30) cc_final: 0.7816 (m-30) REVERT: B 363 TYR cc_start: 0.5901 (p90) cc_final: 0.5413 (p90) REVERT: B 460 LYS cc_start: 0.8270 (pttt) cc_final: 0.7604 (ptmm) REVERT: B 491 TYR cc_start: 0.7312 (m-80) cc_final: 0.7021 (m-80) REVERT: C 6 GLU cc_start: 0.5804 (mp0) cc_final: 0.5421 (mp0) REVERT: C 78 PHE cc_start: 0.5928 (m-80) cc_final: 0.5689 (m-80) REVERT: E 474 ASP cc_start: 0.6448 (p0) cc_final: 0.6219 (t0) outliers start: 35 outliers final: 24 residues processed: 277 average time/residue: 0.1350 time to fit residues: 56.8422 Evaluate side-chains 229 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 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 198 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 146 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS A 471 HIS B 117 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 117 HIS E 344 GLN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.142284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110746 restraints weight = 26455.877| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.68 r_work: 0.3342 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17422 Z= 0.210 Angle : 0.678 9.366 23663 Z= 0.356 Chirality : 0.047 0.223 2642 Planarity : 0.005 0.053 3008 Dihedral : 6.877 42.191 2846 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.96 % Allowed : 8.02 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 2102 helix: 1.66 (0.27), residues: 345 sheet: 0.80 (0.21), residues: 574 loop : -0.20 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 81 TYR 0.027 0.002 TYR E 486 PHE 0.022 0.002 PHE A 439 TRP 0.024 0.002 TRP E 84 HIS 0.017 0.002 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00483 (17371) covalent geometry : angle 0.65547 (23534) SS BOND : bond 0.00435 ( 24) SS BOND : angle 1.87973 ( 48) hydrogen bonds : bond 0.04488 ( 672) hydrogen bonds : angle 5.67377 ( 1899) link_BETA1-4 : bond 0.01058 ( 9) link_BETA1-4 : angle 2.64446 ( 27) link_BETA1-6 : bond 0.00144 ( 3) link_BETA1-6 : angle 1.81884 ( 9) link_NAG-ASN : bond 0.00465 ( 15) link_NAG-ASN : angle 2.93486 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 354 HIS cc_start: 0.7166 (t70) cc_final: 0.6768 (t-170) REVERT: A 389 ASN cc_start: 0.8493 (t0) cc_final: 0.8282 (t0) REVERT: A 431 MET cc_start: 0.8367 (mtp) cc_final: 0.8041 (mtp) REVERT: A 459 VAL cc_start: 0.6711 (OUTLIER) cc_final: 0.6385 (m) REVERT: A 460 LYS cc_start: 0.8328 (pttt) cc_final: 0.7815 (ptmt) REVERT: A 478 MET cc_start: 0.6584 (mmm) cc_final: 0.6327 (mmm) REVERT: H 108 MET cc_start: 0.6137 (tpt) cc_final: 0.5825 (tpt) REVERT: L 24 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.6910 (ttp80) REVERT: B 363 TYR cc_start: 0.5955 (p90) cc_final: 0.5543 (p90) REVERT: B 460 LYS cc_start: 0.8109 (pttt) cc_final: 0.7583 (ptmt) REVERT: B 491 TYR cc_start: 0.7319 (m-80) cc_final: 0.7055 (m-80) REVERT: C 78 PHE cc_start: 0.5905 (m-80) cc_final: 0.5653 (m-80) REVERT: E 262 ARG cc_start: 0.6343 (mmm160) cc_final: 0.6015 (mmp-170) REVERT: E 452 ARG cc_start: 0.6099 (ttp80) cc_final: 0.5753 (ttp-110) REVERT: E 460 LYS cc_start: 0.8260 (ptmt) cc_final: 0.7794 (ptmm) REVERT: E 491 TYR cc_start: 0.7164 (m-80) cc_final: 0.6916 (m-80) REVERT: F 6 GLU cc_start: 0.5269 (mp0) cc_final: 0.4964 (mp0) REVERT: G 24 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7120 (ttm-80) REVERT: G 34 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8072 (m-40) outliers start: 55 outliers final: 36 residues processed: 263 average time/residue: 0.1222 time to fit residues: 48.6528 Evaluate side-chains 244 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 198 VAL Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 459 VAL 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 B residue 208 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 310 LYS Chi-restraints excluded: chain 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 20 THR Chi-restraints excluded: chain G residue 34 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 15 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.0570 chunk 66 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 H 39 GLN H 58 ASN L 38 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN D 38 GLN E 92 ASN ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN G 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.143885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113075 restraints weight = 25969.309| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.55 r_work: 0.3389 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17422 Z= 0.121 Angle : 0.591 9.564 23663 Z= 0.307 Chirality : 0.043 0.230 2642 Planarity : 0.004 0.053 3008 Dihedral : 5.832 39.952 2846 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.94 % Allowed : 9.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2102 helix: 1.80 (0.27), residues: 345 sheet: 0.93 (0.21), residues: 564 loop : -0.20 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 24 TYR 0.021 0.001 TYR B 486 PHE 0.016 0.002 PHE E 467 TRP 0.017 0.001 TRP B 84 HIS 0.009 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00263 (17371) covalent geometry : angle 0.56876 (23534) SS BOND : bond 0.00427 ( 24) SS BOND : angle 1.75028 ( 48) hydrogen bonds : bond 0.03935 ( 672) hydrogen bonds : angle 5.39582 ( 1899) link_BETA1-4 : bond 0.00801 ( 9) link_BETA1-4 : angle 2.43761 ( 27) link_BETA1-6 : bond 0.00054 ( 3) link_BETA1-6 : angle 1.75150 ( 9) link_NAG-ASN : bond 0.00430 ( 15) link_NAG-ASN : angle 2.59909 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.664 Fit side-chains REVERT: A 25 LYS cc_start: 0.8619 (ptpp) cc_final: 0.8410 (ptpt) REVERT: A 354 HIS cc_start: 0.7081 (t70) cc_final: 0.6833 (t-170) REVERT: A 389 ASN cc_start: 0.8518 (t0) cc_final: 0.8240 (t0) REVERT: A 454 GLN cc_start: 0.7969 (mt0) cc_final: 0.7519 (tt0) REVERT: A 460 LYS cc_start: 0.8146 (pttt) cc_final: 0.7630 (ptmt) REVERT: A 491 TYR cc_start: 0.7180 (m-80) cc_final: 0.6806 (m-80) REVERT: H 89 VAL cc_start: 0.6854 (t) cc_final: 0.6365 (t) REVERT: H 108 MET cc_start: 0.6054 (tpt) cc_final: 0.5727 (tpt) REVERT: L 24 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.6839 (ttp80) REVERT: B 355 HIS cc_start: 0.7170 (m90) cc_final: 0.6467 (m-70) REVERT: B 363 TYR cc_start: 0.5890 (p90) cc_final: 0.5446 (p90) REVERT: B 460 LYS cc_start: 0.8162 (pttt) cc_final: 0.7637 (ptmt) REVERT: B 491 TYR cc_start: 0.7271 (m-80) cc_final: 0.7032 (m-80) REVERT: C 53 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7373 (p) REVERT: C 78 PHE cc_start: 0.6088 (m-80) cc_final: 0.5730 (m-80) REVERT: E 262 ARG cc_start: 0.6596 (mmm160) cc_final: 0.6334 (mmm160) REVERT: E 413 MET cc_start: 0.8802 (mtp) cc_final: 0.8363 (ttm) REVERT: E 452 ARG cc_start: 0.6105 (ttp80) cc_final: 0.5491 (ptm-80) REVERT: E 491 TYR cc_start: 0.6978 (m-80) cc_final: 0.6773 (m-80) REVERT: G 24 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.7097 (ttm-80) outliers start: 36 outliers final: 19 residues processed: 265 average time/residue: 0.1344 time to fit residues: 54.3983 Evaluate side-chains 231 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain 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 F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 57 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 100 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS D 3 GLN E 92 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.144177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113189 restraints weight = 25764.409| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.62 r_work: 0.3350 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17422 Z= 0.135 Angle : 0.584 9.096 23663 Z= 0.303 Chirality : 0.043 0.223 2642 Planarity : 0.004 0.051 3008 Dihedral : 5.515 36.930 2846 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.32 % Allowed : 9.69 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.18), residues: 2102 helix: 1.83 (0.27), residues: 345 sheet: 0.98 (0.22), residues: 554 loop : -0.25 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 81 TYR 0.021 0.001 TYR E 486 PHE 0.020 0.002 PHE E 467 TRP 0.017 0.001 TRP B 84 HIS 0.009 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00303 (17371) covalent geometry : angle 0.56325 (23534) SS BOND : bond 0.00441 ( 24) SS BOND : angle 1.78815 ( 48) hydrogen bonds : bond 0.03895 ( 672) hydrogen bonds : angle 5.34391 ( 1899) link_BETA1-4 : bond 0.00808 ( 9) link_BETA1-4 : angle 2.29138 ( 27) link_BETA1-6 : bond 0.00071 ( 3) link_BETA1-6 : angle 1.71215 ( 9) link_NAG-ASN : bond 0.00343 ( 15) link_NAG-ASN : angle 2.53628 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8611 (ptpp) cc_final: 0.8405 (ptpt) REVERT: A 239 MET cc_start: 0.8833 (mtm) cc_final: 0.8479 (mtm) REVERT: A 357 ASN cc_start: 0.6687 (p0) cc_final: 0.6382 (t0) REVERT: A 389 ASN cc_start: 0.8494 (t0) cc_final: 0.8180 (t0) REVERT: A 454 GLN cc_start: 0.7963 (mt0) cc_final: 0.7613 (tt0) REVERT: A 460 LYS cc_start: 0.7955 (pttt) cc_final: 0.7436 (ptmt) REVERT: A 491 TYR cc_start: 0.7296 (m-80) cc_final: 0.6886 (m-80) REVERT: H 58 ASN cc_start: 0.8233 (m-40) cc_final: 0.7741 (m110) REVERT: H 89 VAL cc_start: 0.6799 (t) cc_final: 0.6324 (t) REVERT: H 108 MET cc_start: 0.5992 (tpt) cc_final: 0.5671 (tpt) REVERT: B 363 TYR cc_start: 0.5983 (p90) cc_final: 0.5448 (p90) REVERT: B 460 LYS cc_start: 0.8034 (pttt) cc_final: 0.7517 (ptmt) REVERT: B 491 TYR cc_start: 0.7135 (m-80) cc_final: 0.6931 (m-80) REVERT: C 53 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7341 (p) REVERT: C 78 PHE cc_start: 0.6102 (m-80) cc_final: 0.5647 (m-80) REVERT: E 452 ARG cc_start: 0.6074 (ttp80) cc_final: 0.5866 (ttp-110) REVERT: E 491 TYR cc_start: 0.7013 (m-80) cc_final: 0.6788 (m-80) REVERT: G 24 ARG cc_start: 0.7571 (ttm-80) cc_final: 0.7066 (ttm-80) outliers start: 43 outliers final: 28 residues processed: 250 average time/residue: 0.1439 time to fit residues: 54.4424 Evaluate side-chains 237 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 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 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain E residue 23 THR 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 69 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 382 ASN H 39 GLN D 3 GLN E 92 ASN ** E 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107202 restraints weight = 26092.878| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.62 r_work: 0.3280 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 17422 Z= 0.296 Angle : 0.723 9.240 23663 Z= 0.373 Chirality : 0.048 0.229 2642 Planarity : 0.005 0.060 3008 Dihedral : 6.018 40.720 2846 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.53 % Allowed : 9.96 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.18), residues: 2102 helix: 1.42 (0.26), residues: 344 sheet: 0.65 (0.22), residues: 558 loop : -0.55 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 81 TYR 0.024 0.002 TYR E 486 PHE 0.033 0.003 PHE A 118 TRP 0.028 0.002 TRP E 84 HIS 0.012 0.002 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00701 (17371) covalent geometry : angle 0.70220 (23534) SS BOND : bond 0.00597 ( 24) SS BOND : angle 2.00394 ( 48) hydrogen bonds : bond 0.04509 ( 672) hydrogen bonds : angle 5.57576 ( 1899) link_BETA1-4 : bond 0.00966 ( 9) link_BETA1-4 : angle 2.32219 ( 27) link_BETA1-6 : bond 0.00627 ( 3) link_BETA1-6 : angle 2.06916 ( 9) link_NAG-ASN : bond 0.00600 ( 15) link_NAG-ASN : angle 2.88521 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 ASP cc_start: 0.7573 (t0) cc_final: 0.7355 (t0) REVERT: A 239 MET cc_start: 0.8867 (mtm) cc_final: 0.8498 (mtm) REVERT: A 389 ASN cc_start: 0.8404 (t0) cc_final: 0.8085 (t0) REVERT: A 454 GLN cc_start: 0.8006 (mt0) cc_final: 0.7718 (tt0) REVERT: A 460 LYS cc_start: 0.8168 (pttt) cc_final: 0.7551 (ptmt) REVERT: A 491 TYR cc_start: 0.7383 (m-80) cc_final: 0.6927 (m-80) REVERT: H 108 MET cc_start: 0.6126 (tpt) cc_final: 0.5807 (tpt) REVERT: B 363 TYR cc_start: 0.6199 (p90) cc_final: 0.5614 (p90) REVERT: B 460 LYS cc_start: 0.8115 (pttt) cc_final: 0.7601 (ptmt) REVERT: B 491 TYR cc_start: 0.7289 (m-80) cc_final: 0.7053 (m-80) REVERT: C 53 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7433 (p) REVERT: C 78 PHE cc_start: 0.6161 (m-80) cc_final: 0.5627 (m-80) REVERT: D 24 ARG cc_start: 0.7535 (ttm-80) cc_final: 0.7287 (ttm-80) REVERT: E 354 HIS cc_start: 0.7359 (t-170) cc_final: 0.6519 (t-170) REVERT: E 413 MET cc_start: 0.8435 (mtp) cc_final: 0.8148 (ttm) REVERT: E 431 MET cc_start: 0.8555 (mtp) cc_final: 0.8249 (mtp) REVERT: E 491 TYR cc_start: 0.7100 (m-80) cc_final: 0.6859 (m-80) REVERT: G 24 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7029 (ttp80) outliers start: 47 outliers final: 34 residues processed: 253 average time/residue: 0.1430 time to fit residues: 54.9043 Evaluate side-chains 237 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 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 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 68 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 20 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 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 194 optimal weight: 0.7980 chunk 195 optimal weight: 0.2980 chunk 110 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 355 HIS E 92 ASN E 471 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.142454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.111450 restraints weight = 25560.028| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.61 r_work: 0.3341 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17422 Z= 0.125 Angle : 0.587 12.093 23663 Z= 0.302 Chirality : 0.044 0.227 2642 Planarity : 0.004 0.060 3008 Dihedral : 5.549 39.286 2846 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.62 % Allowed : 11.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.18), residues: 2102 helix: 1.67 (0.26), residues: 345 sheet: 0.81 (0.22), residues: 561 loop : -0.50 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 452 TYR 0.023 0.001 TYR B 486 PHE 0.032 0.002 PHE A 118 TRP 0.015 0.001 TRP A 84 HIS 0.011 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00275 (17371) covalent geometry : angle 0.56888 (23534) SS BOND : bond 0.00476 ( 24) SS BOND : angle 1.65402 ( 48) hydrogen bonds : bond 0.03804 ( 672) hydrogen bonds : angle 5.38880 ( 1899) link_BETA1-4 : bond 0.00699 ( 9) link_BETA1-4 : angle 1.89524 ( 27) link_BETA1-6 : bond 0.00184 ( 3) link_BETA1-6 : angle 1.91875 ( 9) link_NAG-ASN : bond 0.00430 ( 15) link_NAG-ASN : angle 2.46187 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8721 (ptpp) cc_final: 0.7255 (mtpt) REVERT: A 239 MET cc_start: 0.8874 (mtm) cc_final: 0.8487 (mtm) REVERT: A 389 ASN cc_start: 0.8479 (t0) cc_final: 0.8139 (t0) REVERT: A 454 GLN cc_start: 0.8047 (mt0) cc_final: 0.7731 (tt0) REVERT: A 460 LYS cc_start: 0.7832 (pttt) cc_final: 0.7286 (ptmt) REVERT: A 491 TYR cc_start: 0.7270 (m-80) cc_final: 0.6832 (m-80) REVERT: H 58 ASN cc_start: 0.8298 (m-40) cc_final: 0.7788 (t0) REVERT: H 89 VAL cc_start: 0.7004 (t) cc_final: 0.6791 (t) REVERT: B 363 TYR cc_start: 0.6194 (p90) cc_final: 0.5598 (p90) REVERT: B 382 ASN cc_start: 0.8858 (m-40) cc_final: 0.8602 (m110) REVERT: B 460 LYS cc_start: 0.8076 (pttt) cc_final: 0.7522 (ptmt) REVERT: B 491 TYR cc_start: 0.7161 (m-80) cc_final: 0.6934 (m-80) REVERT: C 53 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7434 (p) REVERT: C 78 PHE cc_start: 0.6423 (m-80) cc_final: 0.5869 (m-80) REVERT: D 24 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.7293 (ttm-80) REVERT: E 413 MET cc_start: 0.8377 (mtp) cc_final: 0.8156 (ttm) REVERT: E 452 ARG cc_start: 0.5914 (ttp-110) cc_final: 0.5194 (ptm-80) REVERT: E 491 TYR cc_start: 0.6887 (m-80) cc_final: 0.6668 (m-80) REVERT: G 24 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.6986 (ttp80) outliers start: 30 outliers final: 20 residues processed: 242 average time/residue: 0.1456 time to fit residues: 53.1212 Evaluate side-chains 229 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 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 53 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 409 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 20 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 F residue 53 THR Chi-restraints excluded: chain F residue 57 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 20 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 146 optimal weight: 0.5980 chunk 180 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN E 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108481 restraints weight = 26113.566| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.61 r_work: 0.3275 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17422 Z= 0.232 Angle : 0.668 10.423 23663 Z= 0.342 Chirality : 0.047 0.221 2642 Planarity : 0.005 0.059 3008 Dihedral : 5.766 41.462 2846 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.05 % Allowed : 11.04 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 2102 helix: 1.59 (0.26), residues: 345 sheet: 0.59 (0.22), residues: 568 loop : -0.61 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 81 TYR 0.023 0.002 TYR B 486 PHE 0.041 0.002 PHE A 118 TRP 0.023 0.002 TRP E 84 HIS 0.009 0.002 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00544 (17371) covalent geometry : angle 0.65011 (23534) SS BOND : bond 0.00577 ( 24) SS BOND : angle 1.71050 ( 48) hydrogen bonds : bond 0.04192 ( 672) hydrogen bonds : angle 5.47472 ( 1899) link_BETA1-4 : bond 0.00873 ( 9) link_BETA1-4 : angle 2.05971 ( 27) link_BETA1-6 : bond 0.00372 ( 3) link_BETA1-6 : angle 1.92915 ( 9) link_NAG-ASN : bond 0.00429 ( 15) link_NAG-ASN : angle 2.70130 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8027 (t0) cc_final: 0.7688 (p0) REVERT: A 239 MET cc_start: 0.8893 (mtm) cc_final: 0.8519 (mtm) REVERT: A 389 ASN cc_start: 0.8433 (t0) cc_final: 0.8095 (t0) REVERT: A 460 LYS cc_start: 0.7901 (pttt) cc_final: 0.7241 (ptmt) REVERT: A 491 TYR cc_start: 0.7391 (m-80) cc_final: 0.6916 (m-80) REVERT: H 58 ASN cc_start: 0.8290 (m-40) cc_final: 0.7800 (t0) REVERT: B 363 TYR cc_start: 0.6106 (p90) cc_final: 0.5478 (p90) REVERT: B 382 ASN cc_start: 0.8850 (m-40) cc_final: 0.8594 (m110) REVERT: B 460 LYS cc_start: 0.8115 (pttt) cc_final: 0.7593 (ptmt) REVERT: B 491 TYR cc_start: 0.7317 (m-80) cc_final: 0.7036 (m-80) REVERT: C 53 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7435 (p) REVERT: C 78 PHE cc_start: 0.6412 (m-80) cc_final: 0.5747 (m-80) REVERT: E 354 HIS cc_start: 0.7439 (t-170) cc_final: 0.7082 (t-170) REVERT: E 413 MET cc_start: 0.8461 (mtp) cc_final: 0.8210 (ttm) REVERT: E 431 MET cc_start: 0.8463 (mtp) cc_final: 0.8196 (mtp) REVERT: E 452 ARG cc_start: 0.5964 (ttp-110) cc_final: 0.5714 (ttm110) REVERT: E 491 TYR cc_start: 0.7056 (m-80) cc_final: 0.6799 (m-80) REVERT: F 5 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7875 (mt0) REVERT: G 24 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7023 (ttp80) outliers start: 38 outliers final: 33 residues processed: 237 average time/residue: 0.1429 time to fit residues: 51.0879 Evaluate side-chains 236 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 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 68 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 208 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 C residue 68 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 20 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 409 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain G residue 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 52 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN E 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.139382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109572 restraints weight = 25772.842| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.66 r_work: 0.3318 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17422 Z= 0.167 Angle : 0.612 11.439 23663 Z= 0.314 Chirality : 0.045 0.273 2642 Planarity : 0.004 0.060 3008 Dihedral : 5.588 41.844 2846 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.99 % Allowed : 11.63 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.18), residues: 2102 helix: 1.66 (0.26), residues: 345 sheet: 0.41 (0.22), residues: 586 loop : -0.53 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 81 TYR 0.023 0.002 TYR B 486 PHE 0.035 0.002 PHE A 118 TRP 0.017 0.001 TRP E 84 HIS 0.008 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00388 (17371) covalent geometry : angle 0.59389 (23534) SS BOND : bond 0.00449 ( 24) SS BOND : angle 1.79081 ( 48) hydrogen bonds : bond 0.03912 ( 672) hydrogen bonds : angle 5.40853 ( 1899) link_BETA1-4 : bond 0.00736 ( 9) link_BETA1-4 : angle 1.82863 ( 27) link_BETA1-6 : bond 0.00430 ( 3) link_BETA1-6 : angle 1.93303 ( 9) link_NAG-ASN : bond 0.00382 ( 15) link_NAG-ASN : angle 2.48768 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8046 (t0) cc_final: 0.7761 (p0) REVERT: A 239 MET cc_start: 0.8873 (mtm) cc_final: 0.8489 (mtm) REVERT: A 389 ASN cc_start: 0.8410 (t0) cc_final: 0.8067 (t0) REVERT: A 460 LYS cc_start: 0.7904 (pttt) cc_final: 0.7229 (ptmt) REVERT: A 485 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7879 (p) REVERT: A 491 TYR cc_start: 0.7358 (m-80) cc_final: 0.6874 (m-80) REVERT: H 58 ASN cc_start: 0.8295 (m-40) cc_final: 0.7818 (t0) REVERT: L 42 LYS cc_start: 0.7277 (mttp) cc_final: 0.7077 (mttt) REVERT: B 363 TYR cc_start: 0.5931 (p90) cc_final: 0.5429 (p90) REVERT: B 382 ASN cc_start: 0.8808 (m-40) cc_final: 0.8562 (m110) REVERT: B 460 LYS cc_start: 0.7983 (pttt) cc_final: 0.7416 (ptmt) REVERT: B 491 TYR cc_start: 0.7235 (m-80) cc_final: 0.6966 (m-80) REVERT: C 53 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7483 (p) REVERT: C 78 PHE cc_start: 0.6479 (m-80) cc_final: 0.5839 (m-80) REVERT: E 354 HIS cc_start: 0.7470 (t-170) cc_final: 0.7189 (t-170) REVERT: E 413 MET cc_start: 0.8580 (mtp) cc_final: 0.8260 (ttm) REVERT: E 431 MET cc_start: 0.8396 (mtp) cc_final: 0.8125 (mtp) REVERT: E 491 TYR cc_start: 0.7032 (m-80) cc_final: 0.6753 (m-80) REVERT: G 24 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.6910 (ttp80) outliers start: 37 outliers final: 31 residues processed: 240 average time/residue: 0.1484 time to fit residues: 54.1120 Evaluate side-chains 243 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 176 MET 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 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 20 THR 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 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 107 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109513 restraints weight = 25686.021| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.64 r_work: 0.3317 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 17422 Z= 0.198 Angle : 0.789 59.198 23663 Z= 0.440 Chirality : 0.046 0.300 2642 Planarity : 0.004 0.059 3008 Dihedral : 5.584 41.830 2846 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.88 % Allowed : 11.79 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.18), residues: 2102 helix: 1.65 (0.26), residues: 345 sheet: 0.42 (0.22), residues: 586 loop : -0.53 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 81 TYR 0.022 0.002 TYR B 486 PHE 0.035 0.002 PHE A 118 TRP 0.018 0.001 TRP E 84 HIS 0.008 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00442 (17371) covalent geometry : angle 0.77390 (23534) SS BOND : bond 0.00538 ( 24) SS BOND : angle 2.11074 ( 48) hydrogen bonds : bond 0.03930 ( 672) hydrogen bonds : angle 5.40552 ( 1899) link_BETA1-4 : bond 0.00757 ( 9) link_BETA1-4 : angle 1.83966 ( 27) link_BETA1-6 : bond 0.00272 ( 3) link_BETA1-6 : angle 1.99954 ( 9) link_NAG-ASN : bond 0.00382 ( 15) link_NAG-ASN : angle 2.49546 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8052 (t0) cc_final: 0.7764 (p0) REVERT: A 239 MET cc_start: 0.8876 (mtm) cc_final: 0.8493 (mtm) REVERT: A 389 ASN cc_start: 0.8425 (t0) cc_final: 0.8074 (t0) REVERT: A 460 LYS cc_start: 0.7898 (pttt) cc_final: 0.7220 (ptmt) REVERT: A 485 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7882 (p) REVERT: A 491 TYR cc_start: 0.7364 (m-80) cc_final: 0.6874 (m-80) REVERT: H 58 ASN cc_start: 0.8285 (m-40) cc_final: 0.7810 (t0) REVERT: B 363 TYR cc_start: 0.5922 (p90) cc_final: 0.5422 (p90) REVERT: B 382 ASN cc_start: 0.8807 (m-40) cc_final: 0.8559 (m110) REVERT: B 460 LYS cc_start: 0.7978 (pttt) cc_final: 0.7409 (ptmt) REVERT: B 491 TYR cc_start: 0.7239 (m-80) cc_final: 0.6969 (m-80) REVERT: C 53 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7481 (p) REVERT: C 78 PHE cc_start: 0.6478 (m-80) cc_final: 0.5835 (m-80) REVERT: E 354 HIS cc_start: 0.7439 (t-170) cc_final: 0.7157 (t-170) REVERT: E 413 MET cc_start: 0.8565 (mtp) cc_final: 0.8253 (ttm) REVERT: E 431 MET cc_start: 0.8396 (mtp) cc_final: 0.8139 (mtp) REVERT: E 491 TYR cc_start: 0.7047 (m-80) cc_final: 0.6761 (m-80) REVERT: G 24 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.6910 (ttp80) outliers start: 35 outliers final: 32 residues processed: 232 average time/residue: 0.1408 time to fit residues: 49.6364 Evaluate side-chains 242 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 176 MET 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 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 20 THR 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 118 PHE 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 107 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 173 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109418 restraints weight = 25864.666| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.65 r_work: 0.3316 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 17422 Z= 0.200 Angle : 0.789 59.198 23663 Z= 0.440 Chirality : 0.046 0.300 2642 Planarity : 0.004 0.059 3008 Dihedral : 5.584 41.830 2846 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.83 % Allowed : 11.90 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.18), residues: 2102 helix: 1.65 (0.26), residues: 345 sheet: 0.42 (0.22), residues: 586 loop : -0.53 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 81 TYR 0.022 0.002 TYR B 486 PHE 0.035 0.002 PHE A 118 TRP 0.018 0.001 TRP E 84 HIS 0.008 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00442 (17371) covalent geometry : angle 0.77390 (23534) SS BOND : bond 0.01482 ( 24) SS BOND : angle 2.14105 ( 48) hydrogen bonds : bond 0.03930 ( 672) hydrogen bonds : angle 5.40552 ( 1899) link_BETA1-4 : bond 0.00757 ( 9) link_BETA1-4 : angle 1.83966 ( 27) link_BETA1-6 : bond 0.00272 ( 3) link_BETA1-6 : angle 1.99954 ( 9) link_NAG-ASN : bond 0.00382 ( 15) link_NAG-ASN : angle 2.49546 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4830.63 seconds wall clock time: 83 minutes 45.66 seconds (5025.66 seconds total)