Starting phenix.real_space_refine on Sun May 18 13:30:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp7_41469/05_2025/8tp7_41469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp7_41469/05_2025/8tp7_41469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tp7_41469/05_2025/8tp7_41469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp7_41469/05_2025/8tp7_41469.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp7_41469/05_2025/8tp7_41469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp7_41469/05_2025/8tp7_41469.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.077 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 87 5.16 5 C 10668 2.51 5 N 2859 2.21 5 O 3396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17010 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "B" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "C" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "D" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "E" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "F" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "G" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "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: "C" 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: 10.81, per 1000 atoms: 0.64 Number of scatterers: 17010 At special positions: 0 Unit cell: (117.3, 111.55, 180.55, 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 87 16.00 O 3396 8.00 N 2859 7.00 C 10668 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=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.06 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.06 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.06 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 3 " " NAG K 1 " - " FUC K 3 " NAG-ASN " NAG A 601 " - " ASN A 21 " " NAG A 602 " - " ASN A 33 " " NAG A 603 " - " ASN A 289 " " NAG B 601 " - " ASN B 21 " " NAG B 602 " - " ASN B 33 " " NAG B 603 " - " ASN B 289 " " NAG C 601 " - " ASN C 21 " " NAG C 602 " - " ASN C 33 " " NAG C 603 " - " ASN C 289 " " NAG I 1 " - " ASN A 169 " " NAG J 1 " - " ASN B 169 " " NAG K 1 " - " ASN C 169 " Time building additional restraints: 4.65 Conformation dependent library (CDL) restraints added in 2.3 seconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 51 sheets defined 19.4% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.989A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 125 through 127 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 366 through 387 Processing helix chain 'A' and resid 403 through 456 removed outlier: 3.665A pdb=" N GLN A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.989A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG B 78 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 125 through 127 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 403 through 456 removed outlier: 3.665A pdb=" N GLN B 454 " --> pdb=" O LYS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.989A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 125 through 127 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 366 through 387 Processing helix chain 'C' and resid 403 through 456 removed outlier: 3.664A pdb=" N GLN C 454 " --> pdb=" O LYS C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 482 Processing helix chain 'D' and resid 61 through 65 removed outlier: 4.049A pdb=" N GLU D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY D 65 " --> pdb=" O SER D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 65' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.050A pdb=" N GLU E 64 " --> pdb=" O PRO E 61 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY E 65 " --> pdb=" O SER E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 65' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.049A pdb=" N GLU H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY H 65 " --> pdb=" O SER H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.197A 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: 6.884A pdb=" N LEU A 51 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 5.271A 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: 6.493A pdb=" N LEU A 59 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.283A 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 removed outlier: 6.520A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.520A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 7.802A 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: 7.354A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 10.035A 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 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB3, first strand: chain 'B' and resid 360 through 365 Processing sheet with id=AB4, first strand: chain 'B' and resid 24 through 26 removed outlier: 4.197A pdb=" N GLU B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.884A pdb=" N LEU B 51 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.493A pdb=" N LEU B 59 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.520A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.520A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.355A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'B' and resid 286 through 287 Processing sheet with id=AC5, first strand: chain 'C' and resid 360 through 365 Processing sheet with id=AC6, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.197A pdb=" N GLU C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.883A pdb=" N LEU C 51 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.493A pdb=" N LEU C 59 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.519A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.519A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.355A pdb=" N ALA C 138 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N ASN C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AD7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.175A pdb=" N TRP D 35A" --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN D 50 " --> pdb=" O TRP D 35A" (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.977A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR D 98 " --> pdb=" O THR D 100E" (cutoff:3.500A) removed outlier: 5.708A pdb=" N THR D 100E" --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.175A pdb=" N TRP E 35A" --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN E 50 " --> pdb=" O TRP E 35A" (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.976A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR E 98 " --> pdb=" O THR E 100E" (cutoff:3.500A) removed outlier: 5.708A pdb=" N THR E 100E" --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.488A pdb=" N TRP F 35 " --> pdb=" O ILE F 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 9 through 13 Processing sheet with id=AE6, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.488A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AE9, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.175A pdb=" N TRP H 35A" --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.976A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR H 98 " --> pdb=" O THR H 100E" (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR H 100E" --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.488A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AF6, first strand: chain 'L' and resid 19 through 24 765 hydrogen bonds defined for protein. 1944 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: 6.48 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.25: 2835 1.25 - 1.41: 4628 1.41 - 1.57: 9682 1.57 - 1.72: 138 1.72 - 1.88: 120 Bond restraints: 17403 Sorted by residual: bond pdb=" C TYR G 30C" pdb=" O TYR G 30C" ideal model delta sigma weight residual 1.234 1.093 0.141 1.26e-02 6.30e+03 1.25e+02 bond pdb=" C TYR F 30C" pdb=" O TYR F 30C" ideal model delta sigma weight residual 1.234 1.093 0.141 1.26e-02 6.30e+03 1.25e+02 bond pdb=" C TYR L 30C" pdb=" O TYR L 30C" ideal model delta sigma weight residual 1.234 1.093 0.140 1.26e-02 6.30e+03 1.24e+02 bond pdb=" C ASN L 31 " pdb=" O ASN L 31 " ideal model delta sigma weight residual 1.235 1.107 0.129 1.26e-02 6.30e+03 1.04e+02 bond pdb=" C ASN G 31 " pdb=" O ASN G 31 " ideal model delta sigma weight residual 1.235 1.107 0.128 1.26e-02 6.30e+03 1.04e+02 ... (remaining 17398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.41: 23539 7.41 - 14.83: 61 14.83 - 22.24: 1 22.24 - 29.66: 0 29.66 - 37.07: 3 Bond angle restraints: 23604 Sorted by residual: angle pdb=" N GLY B 342 " pdb=" CA GLY B 342 " pdb=" C GLY B 342 " ideal model delta sigma weight residual 115.32 135.20 -19.88 1.48e+00 4.57e-01 1.80e+02 angle pdb=" C2 NAG C 603 " pdb=" N2 NAG C 603 " pdb=" C7 NAG C 603 " ideal model delta sigma weight residual 124.56 161.63 -37.07 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C2 NAG B 603 " pdb=" N2 NAG B 603 " pdb=" C7 NAG B 603 " ideal model delta sigma weight residual 124.56 161.60 -37.04 3.00e+00 1.11e-01 1.52e+02 angle pdb=" C2 NAG A 603 " pdb=" N2 NAG A 603 " pdb=" C7 NAG A 603 " ideal model delta sigma weight residual 124.56 161.57 -37.01 3.00e+00 1.11e-01 1.52e+02 angle pdb=" N THR B 318 " pdb=" CA THR B 318 " pdb=" C THR B 318 " ideal model delta sigma weight residual 114.04 103.44 10.60 1.24e+00 6.50e-01 7.31e+01 ... (remaining 23599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 10164 17.90 - 35.80: 251 35.80 - 53.69: 73 53.69 - 71.59: 30 71.59 - 89.49: 18 Dihedral angle restraints: 10536 sinusoidal: 4407 harmonic: 6129 Sorted by residual: dihedral pdb=" CB CYS B 64 " pdb=" SG CYS B 64 " pdb=" SG CYS B 76 " pdb=" CB CYS B 76 " ideal model delta sinusoidal sigma weight residual -86.00 -123.20 37.20 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 76 " pdb=" CB CYS A 76 " ideal model delta sinusoidal sigma weight residual -86.00 -123.19 37.19 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS C 76 " pdb=" CB CYS C 76 " ideal model delta sinusoidal sigma weight residual -86.00 -123.15 37.15 1 1.00e+01 1.00e-02 1.95e+01 ... (remaining 10533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1737 0.090 - 0.181: 683 0.181 - 0.271: 115 0.271 - 0.361: 48 0.361 - 0.452: 12 Chirality restraints: 2595 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.27e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.26e+02 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 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 ... (remaining 2592 not shown) Planarity restraints: 3045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 195 " 0.068 2.00e-02 2.50e+03 3.57e-02 2.55e+01 pdb=" CG TYR A 195 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 195 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 195 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 195 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR A 195 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 195 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 195 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 195 " -0.068 2.00e-02 2.50e+03 3.57e-02 2.55e+01 pdb=" CG TYR B 195 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 195 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 195 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 195 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B 195 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 195 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 195 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 195 " 0.068 2.00e-02 2.50e+03 3.55e-02 2.52e+01 pdb=" CG TYR C 195 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR C 195 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR C 195 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR C 195 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR C 195 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR C 195 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 195 " 0.050 2.00e-02 2.50e+03 ... (remaining 3042 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 71 2.57 - 3.15: 13561 3.15 - 3.73: 25559 3.73 - 4.32: 39936 4.32 - 4.90: 63625 Nonbonded interactions: 142752 Sorted by model distance: nonbonded pdb=" CD2 LEU F 4 " pdb=" OD2 ASP F 29 " model vdw 1.987 3.460 nonbonded pdb=" CD2 LEU G 4 " pdb=" OD2 ASP G 29 " model vdw 1.987 3.460 nonbonded pdb=" CD2 LEU L 4 " pdb=" OD2 ASP L 29 " model vdw 1.987 3.460 nonbonded pdb=" OG SER B 136 " pdb=" NE2 GLN B 226 " model vdw 2.058 3.120 nonbonded pdb=" OG SER C 136 " pdb=" NE2 GLN C 226 " model vdw 2.059 3.120 ... (remaining 142747 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: 0.11 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'L' } 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: 2.210 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.410 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 0.141 17445 Z= 1.125 Angle : 1.801 37.074 23706 Z= 1.192 Chirality : 0.102 0.452 2595 Planarity : 0.009 0.046 3033 Dihedral : 10.248 89.486 6576 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2121 helix: 0.89 (0.26), residues: 336 sheet: 0.92 (0.21), residues: 537 loop : 0.40 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.009 TRP L 35 HIS 0.006 0.002 HIS A 183 PHE 0.051 0.006 PHE C 118 TYR 0.068 0.010 TYR A 195 ARG 0.007 0.001 ARG A 93 Details of bonding type rmsd link_NAG-ASN : bond 0.07781 ( 12) link_NAG-ASN : angle 2.00693 ( 36) link_BETA1-4 : bond 0.07505 ( 3) link_BETA1-4 : angle 5.11669 ( 9) hydrogen bonds : bond 0.13533 ( 696) hydrogen bonds : angle 7.28754 ( 1944) link_BETA1-6 : bond 0.05522 ( 3) link_BETA1-6 : angle 2.35665 ( 9) SS BOND : bond 0.01390 ( 24) SS BOND : angle 2.84419 ( 48) covalent geometry : bond 0.02090 (17403) covalent geometry : angle 1.79510 (23604) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8373 (mtp) cc_final: 0.7919 (mtp) REVERT: A 211 LYS cc_start: 0.8671 (tttp) cc_final: 0.8406 (tttm) REVERT: A 402 LEU cc_start: 0.8862 (mt) cc_final: 0.8515 (mm) REVERT: B 88 MET cc_start: 0.8276 (mtp) cc_final: 0.7774 (mtp) REVERT: C 88 MET cc_start: 0.8412 (mtp) cc_final: 0.7887 (mtp) REVERT: C 211 LYS cc_start: 0.8625 (tttp) cc_final: 0.8372 (tttm) REVERT: C 340 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7386 (pp20) REVERT: C 434 GLU cc_start: 0.7964 (tt0) cc_final: 0.7718 (tt0) REVERT: C 438 ASP cc_start: 0.7918 (m-30) cc_final: 0.7533 (m-30) REVERT: G 9 SER cc_start: 0.8356 (t) cc_final: 0.8150 (t) REVERT: L 26 THR cc_start: 0.8301 (p) cc_final: 0.7932 (t) outliers start: 0 outliers final: 2 residues processed: 388 average time/residue: 1.2494 time to fit residues: 541.2901 Evaluate side-chains 224 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 191 GLN A 224 ASN A 458 ASN B 130 HIS B 191 GLN B 210 ASN B 458 ASN C 130 HIS C 391 GLN C 458 ASN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN E 60 ASN G 53 HIS G 69 ASN H 5 GLN H 60 ASN L 69 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109483 restraints weight = 19257.618| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.79 r_work: 0.3126 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17445 Z= 0.159 Angle : 0.615 5.727 23706 Z= 0.342 Chirality : 0.044 0.187 2595 Planarity : 0.004 0.038 3033 Dihedral : 6.925 86.311 2686 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.94 % Allowed : 8.72 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.17), residues: 2121 helix: 2.37 (0.28), residues: 333 sheet: 0.95 (0.22), residues: 543 loop : -0.19 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 35A HIS 0.002 0.001 HIS C 354 PHE 0.026 0.002 PHE B 118 TYR 0.019 0.002 TYR E 35 ARG 0.004 0.001 ARG A 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 12) link_NAG-ASN : angle 1.45109 ( 36) link_BETA1-4 : bond 0.00165 ( 3) link_BETA1-4 : angle 2.52624 ( 9) hydrogen bonds : bond 0.05375 ( 696) hydrogen bonds : angle 5.57118 ( 1944) link_BETA1-6 : bond 0.00857 ( 3) link_BETA1-6 : angle 0.97119 ( 9) SS BOND : bond 0.00252 ( 24) SS BOND : angle 1.34729 ( 48) covalent geometry : bond 0.00335 (17403) covalent geometry : angle 0.60890 (23604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8797 (mtp) cc_final: 0.8268 (mtp) REVERT: A 210 ASN cc_start: 0.8792 (t0) cc_final: 0.8485 (t0) REVERT: A 211 LYS cc_start: 0.8843 (tttp) cc_final: 0.7865 (tttm) REVERT: A 310 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8436 (mtmt) REVERT: A 340 GLU cc_start: 0.8603 (mm-30) cc_final: 0.6871 (pp20) REVERT: A 438 ASP cc_start: 0.8255 (m-30) cc_final: 0.7878 (m-30) REVERT: A 445 LYS cc_start: 0.7472 (mttt) cc_final: 0.7126 (mtpp) REVERT: B 88 MET cc_start: 0.8714 (mtp) cc_final: 0.8339 (mtp) REVERT: B 210 ASN cc_start: 0.8698 (t0) cc_final: 0.8324 (t0) REVERT: B 340 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6308 (pp20) REVERT: B 344 GLN cc_start: 0.8365 (mt0) cc_final: 0.7923 (mm-40) REVERT: B 402 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8000 (mm) REVERT: B 438 ASP cc_start: 0.8178 (m-30) cc_final: 0.7858 (m-30) REVERT: B 445 LYS cc_start: 0.7653 (mttt) cc_final: 0.7247 (mtpt) REVERT: C 211 LYS cc_start: 0.8786 (tttp) cc_final: 0.8191 (tttm) REVERT: C 340 GLU cc_start: 0.8195 (mm-30) cc_final: 0.6671 (pp20) REVERT: C 344 GLN cc_start: 0.8453 (mt0) cc_final: 0.7922 (mt0) REVERT: C 434 GLU cc_start: 0.8107 (tt0) cc_final: 0.7869 (tt0) REVERT: C 435 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7307 (mtt180) REVERT: C 438 ASP cc_start: 0.8100 (m-30) cc_final: 0.7657 (m-30) REVERT: C 445 LYS cc_start: 0.7612 (mttt) cc_final: 0.7009 (mtpp) REVERT: D 6 GLU cc_start: 0.7849 (mp0) cc_final: 0.7623 (mp0) REVERT: E 5 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8271 (mm-40) REVERT: H 6 GLU cc_start: 0.7723 (mp0) cc_final: 0.7340 (mp0) outliers start: 36 outliers final: 19 residues processed: 295 average time/residue: 1.0967 time to fit residues: 367.6108 Evaluate side-chains 245 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain H residue 25 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 21 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 chunk 157 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 186 ASN A 226 GLN B 196 GLN B 389 ASN C 322 ASN C 379 ASN C 479 ASN E 5 GLN E 60 ASN E 77 GLN F 38 ASN H 60 ASN H 77 GLN L 38 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106101 restraints weight = 19648.467| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.82 r_work: 0.3103 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17445 Z= 0.197 Angle : 0.609 10.918 23706 Z= 0.330 Chirality : 0.045 0.150 2595 Planarity : 0.004 0.039 3033 Dihedral : 6.560 85.172 2684 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.45 % Allowed : 10.66 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2121 helix: 2.45 (0.28), residues: 333 sheet: 0.62 (0.20), residues: 594 loop : -0.29 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 35A HIS 0.016 0.002 HIS C 471 PHE 0.031 0.003 PHE B 118 TYR 0.017 0.002 TYR D 100F ARG 0.003 0.000 ARG D 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 12) link_NAG-ASN : angle 1.16574 ( 36) link_BETA1-4 : bond 0.00452 ( 3) link_BETA1-4 : angle 2.10036 ( 9) hydrogen bonds : bond 0.04932 ( 696) hydrogen bonds : angle 5.23233 ( 1944) link_BETA1-6 : bond 0.00537 ( 3) link_BETA1-6 : angle 1.01820 ( 9) SS BOND : bond 0.00453 ( 24) SS BOND : angle 1.24214 ( 48) covalent geometry : bond 0.00469 (17403) covalent geometry : angle 0.60400 (23604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 252 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8775 (mtp) cc_final: 0.8323 (mtp) REVERT: A 157 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8461 (tttt) REVERT: A 210 ASN cc_start: 0.8817 (t0) cc_final: 0.8553 (t0) REVERT: A 211 LYS cc_start: 0.8884 (tttp) cc_final: 0.8287 (tttm) REVERT: A 310 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8494 (mtmt) REVERT: A 340 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.6820 (pp20) REVERT: A 404 ARG cc_start: 0.8343 (mmp-170) cc_final: 0.8060 (mmp-170) REVERT: A 438 ASP cc_start: 0.8312 (m-30) cc_final: 0.7954 (m-30) REVERT: A 445 LYS cc_start: 0.7808 (mttt) cc_final: 0.7523 (mtmt) REVERT: A 490 LYS cc_start: 0.7478 (ttpt) cc_final: 0.7055 (ttmm) REVERT: B 151 MET cc_start: 0.9266 (mmp) cc_final: 0.9049 (mmp) REVERT: B 210 ASN cc_start: 0.8766 (t0) cc_final: 0.8539 (t0) REVERT: B 340 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6441 (pp20) REVERT: B 402 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8182 (mm) REVERT: B 445 LYS cc_start: 0.7677 (mttt) cc_final: 0.7282 (mtpt) REVERT: B 460 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7547 (mtmt) REVERT: C 50 LYS cc_start: 0.7217 (mttt) cc_final: 0.6839 (mtmt) REVERT: C 211 LYS cc_start: 0.8802 (tttp) cc_final: 0.8204 (tttm) REVERT: C 340 GLU cc_start: 0.8285 (mm-30) cc_final: 0.6623 (pp20) REVERT: C 344 GLN cc_start: 0.8593 (mt0) cc_final: 0.8110 (mt0) REVERT: C 386 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7756 (mt-10) REVERT: C 404 ARG cc_start: 0.8444 (mmp-170) cc_final: 0.8156 (mmp-170) REVERT: C 434 GLU cc_start: 0.8184 (tt0) cc_final: 0.7963 (tt0) REVERT: C 435 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7223 (mtp180) REVERT: C 438 ASP cc_start: 0.8193 (m-30) cc_final: 0.7865 (m-30) REVERT: C 441 ASP cc_start: 0.7971 (m-30) cc_final: 0.7695 (m-30) REVERT: C 445 LYS cc_start: 0.7623 (mttt) cc_final: 0.7096 (mtpp) REVERT: C 449 ASP cc_start: 0.7701 (m-30) cc_final: 0.7499 (m-30) REVERT: C 483 ASN cc_start: 0.7506 (t0) cc_final: 0.7046 (m110) REVERT: E 5 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8230 (mm-40) REVERT: H 6 GLU cc_start: 0.7830 (mp0) cc_final: 0.7475 (mp0) REVERT: H 105 GLN cc_start: 0.7599 (pm20) cc_final: 0.7371 (pm20) REVERT: L 74 SER cc_start: 0.8313 (t) cc_final: 0.7849 (m) outliers start: 64 outliers final: 35 residues processed: 288 average time/residue: 1.1453 time to fit residues: 371.2700 Evaluate side-chains 261 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 134 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 201 optimal weight: 0.0010 chunk 120 optimal weight: 0.0670 chunk 187 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.8130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN B 355 HIS C 160 ASN C 355 HIS E 5 GLN H 77 GLN L 69 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107624 restraints weight = 19669.420| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.78 r_work: 0.3128 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17445 Z= 0.130 Angle : 0.515 5.413 23706 Z= 0.281 Chirality : 0.042 0.140 2595 Planarity : 0.004 0.031 3033 Dihedral : 6.260 85.326 2684 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.32 % Allowed : 12.76 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2121 helix: 2.70 (0.27), residues: 333 sheet: 0.62 (0.21), residues: 591 loop : -0.31 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 35A HIS 0.024 0.001 HIS B 471 PHE 0.023 0.002 PHE B 118 TYR 0.012 0.001 TYR E 100F ARG 0.003 0.000 ARG B 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 12) link_NAG-ASN : angle 1.27542 ( 36) link_BETA1-4 : bond 0.00365 ( 3) link_BETA1-4 : angle 1.84354 ( 9) hydrogen bonds : bond 0.04376 ( 696) hydrogen bonds : angle 4.99176 ( 1944) link_BETA1-6 : bond 0.00520 ( 3) link_BETA1-6 : angle 1.01286 ( 9) SS BOND : bond 0.00203 ( 24) SS BOND : angle 1.01677 ( 48) covalent geometry : bond 0.00298 (17403) covalent geometry : angle 0.51048 (23604) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 239 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 CYS cc_start: 0.7210 (m) cc_final: 0.6843 (m) REVERT: A 88 MET cc_start: 0.8671 (mtp) cc_final: 0.8400 (mtp) REVERT: A 211 LYS cc_start: 0.8890 (tttp) cc_final: 0.7969 (tttm) REVERT: A 310 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8432 (mtmt) REVERT: A 340 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.6855 (pp20) REVERT: A 344 GLN cc_start: 0.8690 (mt0) cc_final: 0.8316 (mm-40) REVERT: A 404 ARG cc_start: 0.8361 (mmp-170) cc_final: 0.8083 (mmp-170) REVERT: A 413 MET cc_start: 0.8785 (ttp) cc_final: 0.8572 (ttp) REVERT: A 414 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7933 (mp0) REVERT: A 445 LYS cc_start: 0.7671 (mttt) cc_final: 0.7426 (mtmt) REVERT: A 483 ASN cc_start: 0.7731 (t0) cc_final: 0.7351 (m110) REVERT: A 490 LYS cc_start: 0.7469 (ttpt) cc_final: 0.7102 (ttmm) REVERT: B 340 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6400 (pp20) REVERT: B 344 GLN cc_start: 0.8773 (mt0) cc_final: 0.8162 (mm-40) REVERT: B 388 MET cc_start: 0.8663 (mmm) cc_final: 0.8429 (mmt) REVERT: B 402 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8150 (mm) REVERT: B 441 ASP cc_start: 0.7982 (m-30) cc_final: 0.7759 (m-30) REVERT: B 445 LYS cc_start: 0.7489 (mttt) cc_final: 0.7117 (mtpt) REVERT: B 460 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7557 (mtmt) REVERT: C 50 LYS cc_start: 0.7186 (mttt) cc_final: 0.6869 (mtmt) REVERT: C 137 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7518 (mpt180) REVERT: C 340 GLU cc_start: 0.8249 (mm-30) cc_final: 0.6581 (pp20) REVERT: C 344 GLN cc_start: 0.8624 (mt0) cc_final: 0.8185 (mt0) REVERT: C 434 GLU cc_start: 0.8139 (tt0) cc_final: 0.7876 (tt0) REVERT: C 435 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7174 (mtp180) REVERT: C 438 ASP cc_start: 0.8201 (m-30) cc_final: 0.7861 (m-30) REVERT: C 441 ASP cc_start: 0.7989 (m-30) cc_final: 0.7632 (m-30) REVERT: C 445 LYS cc_start: 0.7512 (mttt) cc_final: 0.7118 (mtpt) REVERT: C 449 ASP cc_start: 0.7727 (m-30) cc_final: 0.7437 (m-30) REVERT: C 483 ASN cc_start: 0.7459 (t0) cc_final: 0.7006 (m110) REVERT: D 3 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: E 5 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7982 (mm-40) REVERT: E 6 GLU cc_start: 0.7697 (mp0) cc_final: 0.7350 (mp0) REVERT: H 6 GLU cc_start: 0.7765 (mp0) cc_final: 0.7330 (mp0) REVERT: H 105 GLN cc_start: 0.7451 (pm20) cc_final: 0.7102 (pm20) outliers start: 43 outliers final: 27 residues processed: 266 average time/residue: 1.1597 time to fit residues: 346.4038 Evaluate side-chains 246 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN E 5 GLN E 60 ASN G 38 ASN L 53 HIS L 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105400 restraints weight = 19921.463| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.78 r_work: 0.3083 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17445 Z= 0.214 Angle : 0.586 6.241 23706 Z= 0.314 Chirality : 0.044 0.142 2595 Planarity : 0.004 0.038 3033 Dihedral : 6.336 84.342 2684 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.66 % Allowed : 11.85 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.18), residues: 2121 helix: 2.61 (0.27), residues: 333 sheet: 0.40 (0.21), residues: 597 loop : -0.40 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 103 HIS 0.010 0.001 HIS B 471 PHE 0.030 0.003 PHE C 118 TYR 0.016 0.002 TYR D 100F ARG 0.004 0.001 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 12) link_NAG-ASN : angle 1.38103 ( 36) link_BETA1-4 : bond 0.00448 ( 3) link_BETA1-4 : angle 2.03691 ( 9) hydrogen bonds : bond 0.04686 ( 696) hydrogen bonds : angle 5.05782 ( 1944) link_BETA1-6 : bond 0.00424 ( 3) link_BETA1-6 : angle 0.96453 ( 9) SS BOND : bond 0.00253 ( 24) SS BOND : angle 1.09725 ( 48) covalent geometry : bond 0.00520 (17403) covalent geometry : angle 0.58068 (23604) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 235 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8825 (mtp) cc_final: 0.7899 (ttm) REVERT: A 211 LYS cc_start: 0.8893 (tttp) cc_final: 0.7919 (tttm) REVERT: A 310 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8450 (mtmt) REVERT: A 340 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.6809 (pp20) REVERT: A 404 ARG cc_start: 0.8308 (mmp-170) cc_final: 0.7990 (mmp-170) REVERT: A 414 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8059 (mp0) REVERT: A 445 LYS cc_start: 0.7728 (mttt) cc_final: 0.7515 (mtmt) REVERT: A 483 ASN cc_start: 0.7764 (t0) cc_final: 0.7303 (m110) REVERT: A 490 LYS cc_start: 0.7746 (ttpt) cc_final: 0.7527 (ttpt) REVERT: B 64 CYS cc_start: 0.7060 (m) cc_final: 0.6666 (m) REVERT: B 137 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8162 (mmt90) REVERT: B 310 LYS cc_start: 0.8772 (mtmm) cc_final: 0.8563 (mtmt) REVERT: B 340 GLU cc_start: 0.7690 (mm-30) cc_final: 0.6418 (pp20) REVERT: B 402 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8148 (mm) REVERT: B 445 LYS cc_start: 0.7532 (mttt) cc_final: 0.7145 (mtpt) REVERT: B 460 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7500 (mtmt) REVERT: C 50 LYS cc_start: 0.7390 (mttt) cc_final: 0.6919 (mtmt) REVERT: C 64 CYS cc_start: 0.7393 (m) cc_final: 0.6992 (m) REVERT: C 137 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7529 (mpt180) REVERT: C 340 GLU cc_start: 0.8262 (mm-30) cc_final: 0.6483 (pp20) REVERT: C 434 GLU cc_start: 0.8182 (tt0) cc_final: 0.7939 (tt0) REVERT: C 435 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7081 (mtp180) REVERT: C 441 ASP cc_start: 0.7952 (m-30) cc_final: 0.7553 (m-30) REVERT: C 445 LYS cc_start: 0.7587 (mttt) cc_final: 0.7181 (mtpt) REVERT: C 449 ASP cc_start: 0.7681 (m-30) cc_final: 0.7379 (m-30) REVERT: C 483 ASN cc_start: 0.7516 (t0) cc_final: 0.6997 (m110) REVERT: D 34 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: E 5 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7856 (mm-40) REVERT: E 6 GLU cc_start: 0.7597 (mp0) cc_final: 0.7255 (mp0) REVERT: H 6 GLU cc_start: 0.7786 (mp0) cc_final: 0.7319 (mp0) REVERT: H 70 SER cc_start: 0.8544 (t) cc_final: 0.8166 (m) outliers start: 68 outliers final: 49 residues processed: 274 average time/residue: 1.1843 time to fit residues: 365.9899 Evaluate side-chains 281 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 160 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 69 optimal weight: 0.0570 chunk 5 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 169 optimal weight: 0.0670 chunk 64 optimal weight: 4.9990 chunk 56 optimal weight: 0.0000 chunk 17 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS E 5 GLN L 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108943 restraints weight = 19775.790| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.77 r_work: 0.3145 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17445 Z= 0.091 Angle : 0.470 5.059 23706 Z= 0.255 Chirality : 0.040 0.156 2595 Planarity : 0.003 0.030 3033 Dihedral : 5.951 85.783 2684 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.26 % Allowed : 13.68 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2121 helix: 2.93 (0.28), residues: 333 sheet: 0.57 (0.21), residues: 606 loop : -0.31 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35A HIS 0.008 0.001 HIS B 471 PHE 0.019 0.001 PHE A 118 TYR 0.009 0.001 TYR D 35 ARG 0.004 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 12) link_NAG-ASN : angle 1.34473 ( 36) link_BETA1-4 : bond 0.00388 ( 3) link_BETA1-4 : angle 1.68681 ( 9) hydrogen bonds : bond 0.03945 ( 696) hydrogen bonds : angle 4.80157 ( 1944) link_BETA1-6 : bond 0.00429 ( 3) link_BETA1-6 : angle 1.08585 ( 9) SS BOND : bond 0.00255 ( 24) SS BOND : angle 0.71076 ( 48) covalent geometry : bond 0.00188 (17403) covalent geometry : angle 0.46502 (23604) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8593 (mtpt) cc_final: 0.8317 (mtmt) REVERT: A 340 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.6706 (pp20) REVERT: A 402 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8044 (mm) REVERT: A 404 ARG cc_start: 0.8246 (mmp-170) cc_final: 0.7928 (mmp-170) REVERT: A 413 MET cc_start: 0.8749 (ttp) cc_final: 0.8439 (ttp) REVERT: A 414 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7921 (mp0) REVERT: A 438 ASP cc_start: 0.8261 (m-30) cc_final: 0.7895 (m-30) REVERT: A 445 LYS cc_start: 0.7530 (mttt) cc_final: 0.7208 (mtmt) REVERT: A 483 ASN cc_start: 0.7770 (t0) cc_final: 0.7362 (m110) REVERT: A 490 LYS cc_start: 0.7801 (ttpt) cc_final: 0.7570 (ttpp) REVERT: B 195 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.7443 (m-80) REVERT: B 335 ILE cc_start: 0.6562 (tt) cc_final: 0.6337 (tt) REVERT: B 340 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6344 (pp20) REVERT: B 344 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8524 (mm-40) REVERT: B 402 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8085 (mm) REVERT: B 441 ASP cc_start: 0.7968 (m-30) cc_final: 0.7734 (m-30) REVERT: B 445 LYS cc_start: 0.7377 (mttt) cc_final: 0.6966 (mtpt) REVERT: B 460 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7538 (mtmt) REVERT: B 479 ASN cc_start: 0.7553 (m110) cc_final: 0.7276 (m-40) REVERT: C 50 LYS cc_start: 0.7267 (mttt) cc_final: 0.6815 (mtmt) REVERT: C 137 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7523 (mpt180) REVERT: C 340 GLU cc_start: 0.8300 (mm-30) cc_final: 0.6419 (pp20) REVERT: C 344 GLN cc_start: 0.8737 (mt0) cc_final: 0.8372 (mm-40) REVERT: C 431 MET cc_start: 0.7778 (mtt) cc_final: 0.7502 (mtp) REVERT: C 434 GLU cc_start: 0.8088 (tt0) cc_final: 0.7853 (tt0) REVERT: C 435 ARG cc_start: 0.7818 (mtm110) cc_final: 0.7056 (mtp180) REVERT: C 441 ASP cc_start: 0.7883 (m-30) cc_final: 0.7500 (m-30) REVERT: C 445 LYS cc_start: 0.7413 (mttt) cc_final: 0.7021 (mtpt) REVERT: C 449 ASP cc_start: 0.7605 (m-30) cc_final: 0.7310 (m-30) REVERT: C 483 ASN cc_start: 0.7494 (t0) cc_final: 0.6996 (m110) REVERT: D 34 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: E 5 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7836 (mm-40) REVERT: E 6 GLU cc_start: 0.7509 (mp0) cc_final: 0.7098 (mp0) REVERT: E 81 LYS cc_start: 0.7995 (mttp) cc_final: 0.7788 (mttm) REVERT: H 6 GLU cc_start: 0.7670 (mp0) cc_final: 0.7236 (mp0) REVERT: H 105 GLN cc_start: 0.7483 (pm20) cc_final: 0.7105 (pm20) REVERT: L 70 THR cc_start: 0.8606 (m) cc_final: 0.8298 (m) outliers start: 42 outliers final: 20 residues processed: 266 average time/residue: 1.1419 time to fit residues: 342.1990 Evaluate side-chains 242 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 1 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 186 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN E 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103077 restraints weight = 19873.576| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.77 r_work: 0.3063 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 17445 Z= 0.269 Angle : 0.636 6.747 23706 Z= 0.337 Chirality : 0.046 0.179 2595 Planarity : 0.004 0.047 3033 Dihedral : 6.322 84.887 2684 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.72 % Allowed : 12.71 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2121 helix: 2.68 (0.27), residues: 330 sheet: 0.36 (0.21), residues: 555 loop : -0.50 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 343 HIS 0.007 0.002 HIS B 471 PHE 0.037 0.003 PHE C 118 TYR 0.020 0.003 TYR E 102 ARG 0.004 0.001 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 12) link_NAG-ASN : angle 1.56565 ( 36) link_BETA1-4 : bond 0.00377 ( 3) link_BETA1-4 : angle 2.13771 ( 9) hydrogen bonds : bond 0.04834 ( 696) hydrogen bonds : angle 5.10681 ( 1944) link_BETA1-6 : bond 0.00386 ( 3) link_BETA1-6 : angle 0.98219 ( 9) SS BOND : bond 0.00317 ( 24) SS BOND : angle 1.28107 ( 48) covalent geometry : bond 0.00658 (17403) covalent geometry : angle 0.63062 (23604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 231 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 CYS cc_start: 0.7173 (m) cc_final: 0.6799 (m) REVERT: A 310 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8498 (mtmt) REVERT: A 340 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.6824 (pp20) REVERT: A 402 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8126 (mm) REVERT: A 404 ARG cc_start: 0.8346 (mmp-170) cc_final: 0.8010 (mmp-170) REVERT: A 413 MET cc_start: 0.8821 (ttp) cc_final: 0.8593 (ttp) REVERT: A 414 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8129 (mp0) REVERT: A 445 LYS cc_start: 0.7868 (mttt) cc_final: 0.7545 (mtmt) REVERT: A 483 ASN cc_start: 0.7842 (t0) cc_final: 0.7350 (m110) REVERT: A 490 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7529 (ttpt) REVERT: B 137 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8175 (mmt90) REVERT: B 195 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: B 340 GLU cc_start: 0.7820 (mm-30) cc_final: 0.6486 (pp20) REVERT: B 346 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8122 (ttm) REVERT: B 402 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8252 (mm) REVERT: B 445 LYS cc_start: 0.7589 (mttt) cc_final: 0.7204 (mtpt) REVERT: B 460 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7572 (mtmt) REVERT: B 479 ASN cc_start: 0.7676 (m110) cc_final: 0.7382 (m-40) REVERT: C 50 LYS cc_start: 0.7401 (mttt) cc_final: 0.6986 (mtpt) REVERT: C 137 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7604 (mpt180) REVERT: C 340 GLU cc_start: 0.8297 (mm-30) cc_final: 0.6552 (pp20) REVERT: C 434 GLU cc_start: 0.8262 (tt0) cc_final: 0.8022 (tt0) REVERT: C 435 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7203 (mtp180) REVERT: C 441 ASP cc_start: 0.8051 (m-30) cc_final: 0.7684 (m-30) REVERT: C 445 LYS cc_start: 0.7666 (mttt) cc_final: 0.7250 (mtpt) REVERT: C 449 ASP cc_start: 0.7716 (m-30) cc_final: 0.7411 (m-30) REVERT: C 483 ASN cc_start: 0.7578 (t0) cc_final: 0.7089 (m110) REVERT: D 34 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: E 5 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7970 (mm-40) REVERT: E 6 GLU cc_start: 0.7735 (mp0) cc_final: 0.7394 (mp0) REVERT: E 81 LYS cc_start: 0.8223 (mttp) cc_final: 0.8019 (mttm) REVERT: G 103 LYS cc_start: 0.7902 (ttmm) cc_final: 0.7309 (tptm) REVERT: H 6 GLU cc_start: 0.7843 (mp0) cc_final: 0.7348 (mp0) REVERT: H 34 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: H 70 SER cc_start: 0.8524 (t) cc_final: 0.8099 (m) REVERT: H 105 GLN cc_start: 0.7601 (pm20) cc_final: 0.7215 (pm20) outliers start: 69 outliers final: 44 residues processed: 269 average time/residue: 1.1093 time to fit residues: 337.4484 Evaluate side-chains 279 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 224 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 74 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 195 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN L 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106551 restraints weight = 19792.459| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.78 r_work: 0.3110 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17445 Z= 0.120 Angle : 0.511 8.343 23706 Z= 0.274 Chirality : 0.041 0.164 2595 Planarity : 0.003 0.032 3033 Dihedral : 6.025 86.585 2684 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.48 % Allowed : 14.27 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2121 helix: 2.93 (0.28), residues: 330 sheet: 0.43 (0.21), residues: 564 loop : -0.39 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 35A HIS 0.006 0.001 HIS B 471 PHE 0.022 0.002 PHE C 118 TYR 0.014 0.001 TYR E 102 ARG 0.005 0.000 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 12) link_NAG-ASN : angle 1.47109 ( 36) link_BETA1-4 : bond 0.00396 ( 3) link_BETA1-4 : angle 1.78066 ( 9) hydrogen bonds : bond 0.04125 ( 696) hydrogen bonds : angle 4.95753 ( 1944) link_BETA1-6 : bond 0.00485 ( 3) link_BETA1-6 : angle 1.09001 ( 9) SS BOND : bond 0.00190 ( 24) SS BOND : angle 1.49009 ( 48) covalent geometry : bond 0.00273 (17403) covalent geometry : angle 0.50227 (23604) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.6671 (pp20) REVERT: A 402 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8088 (mm) REVERT: A 404 ARG cc_start: 0.8227 (mmp-170) cc_final: 0.7909 (mmp-170) REVERT: A 413 MET cc_start: 0.8793 (ttp) cc_final: 0.8460 (ttp) REVERT: A 414 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7938 (mp0) REVERT: A 445 LYS cc_start: 0.7590 (mttt) cc_final: 0.7280 (mtmt) REVERT: A 483 ASN cc_start: 0.7786 (t0) cc_final: 0.7337 (m110) REVERT: A 490 LYS cc_start: 0.7913 (ttpt) cc_final: 0.7663 (ttpp) REVERT: B 195 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: B 340 GLU cc_start: 0.7726 (mm-30) cc_final: 0.6334 (pp20) REVERT: B 402 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8173 (mm) REVERT: B 445 LYS cc_start: 0.7473 (mttt) cc_final: 0.7083 (mtpt) REVERT: B 460 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7536 (mtmt) REVERT: B 479 ASN cc_start: 0.7644 (m110) cc_final: 0.7363 (m-40) REVERT: C 50 LYS cc_start: 0.7307 (mttt) cc_final: 0.6898 (mtpt) REVERT: C 137 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7531 (mpt180) REVERT: C 340 GLU cc_start: 0.8298 (mm-30) cc_final: 0.6416 (pp20) REVERT: C 344 GLN cc_start: 0.8662 (mt0) cc_final: 0.8335 (mt0) REVERT: C 432 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8118 (mm-30) REVERT: C 434 GLU cc_start: 0.8141 (tt0) cc_final: 0.7891 (tt0) REVERT: C 435 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7022 (mtp180) REVERT: C 441 ASP cc_start: 0.7943 (m-30) cc_final: 0.7530 (m-30) REVERT: C 445 LYS cc_start: 0.7523 (mttt) cc_final: 0.7120 (mtpt) REVERT: C 449 ASP cc_start: 0.7634 (m-30) cc_final: 0.7331 (m-30) REVERT: C 483 ASN cc_start: 0.7184 (t0) cc_final: 0.6843 (m110) REVERT: D 34 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: E 5 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7914 (mm-40) REVERT: E 6 GLU cc_start: 0.7691 (mp0) cc_final: 0.7343 (mp0) REVERT: E 81 LYS cc_start: 0.8105 (mttp) cc_final: 0.7872 (mttp) REVERT: H 6 GLU cc_start: 0.7820 (mp0) cc_final: 0.7362 (mp0) REVERT: H 34 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: H 70 SER cc_start: 0.8390 (t) cc_final: 0.7912 (m) REVERT: H 105 GLN cc_start: 0.7524 (pm20) cc_final: 0.7135 (pm20) REVERT: L 70 THR cc_start: 0.8601 (m) cc_final: 0.8292 (m) outliers start: 46 outliers final: 26 residues processed: 253 average time/residue: 1.1178 time to fit residues: 319.9066 Evaluate side-chains 249 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 84 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 47 optimal weight: 0.2980 chunk 151 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 127 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN L 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.134440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106908 restraints weight = 19936.101| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.77 r_work: 0.3100 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17445 Z= 0.148 Angle : 0.538 9.090 23706 Z= 0.286 Chirality : 0.042 0.169 2595 Planarity : 0.004 0.032 3033 Dihedral : 6.028 87.160 2684 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.80 % Allowed : 13.84 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2121 helix: 2.87 (0.28), residues: 330 sheet: 0.43 (0.21), residues: 564 loop : -0.42 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 35A HIS 0.006 0.001 HIS B 471 PHE 0.026 0.002 PHE C 118 TYR 0.013 0.002 TYR E 102 ARG 0.005 0.000 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 12) link_NAG-ASN : angle 1.49203 ( 36) link_BETA1-4 : bond 0.00383 ( 3) link_BETA1-4 : angle 1.84106 ( 9) hydrogen bonds : bond 0.04183 ( 696) hydrogen bonds : angle 5.00503 ( 1944) link_BETA1-6 : bond 0.00384 ( 3) link_BETA1-6 : angle 1.06441 ( 9) SS BOND : bond 0.00190 ( 24) SS BOND : angle 2.01594 ( 48) covalent geometry : bond 0.00355 (17403) covalent geometry : angle 0.52618 (23604) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.6768 (pp20) REVERT: A 402 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8149 (mm) REVERT: A 404 ARG cc_start: 0.8275 (mmp-170) cc_final: 0.7966 (mmp-170) REVERT: A 413 MET cc_start: 0.8786 (ttp) cc_final: 0.8499 (ttp) REVERT: A 414 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7992 (mp0) REVERT: A 445 LYS cc_start: 0.7656 (mttt) cc_final: 0.7328 (mtmt) REVERT: A 483 ASN cc_start: 0.7798 (t0) cc_final: 0.7363 (m110) REVERT: A 490 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7695 (ttpp) REVERT: B 195 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: B 340 GLU cc_start: 0.7760 (mm-30) cc_final: 0.6458 (pp20) REVERT: B 402 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8184 (mm) REVERT: B 445 LYS cc_start: 0.7533 (mttt) cc_final: 0.7146 (mtpt) REVERT: B 460 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7573 (mtmt) REVERT: B 479 ASN cc_start: 0.7588 (m110) cc_final: 0.7303 (m-40) REVERT: C 50 LYS cc_start: 0.7429 (mttt) cc_final: 0.7187 (mtpm) REVERT: C 64 CYS cc_start: 0.7259 (m) cc_final: 0.6883 (m) REVERT: C 137 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7596 (mpt180) REVERT: C 340 GLU cc_start: 0.8230 (mm-30) cc_final: 0.6494 (pp20) REVERT: C 344 GLN cc_start: 0.8697 (mt0) cc_final: 0.8378 (mt0) REVERT: C 432 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8221 (mm-30) REVERT: C 434 GLU cc_start: 0.8175 (tt0) cc_final: 0.7937 (tt0) REVERT: C 435 ARG cc_start: 0.7872 (mtm110) cc_final: 0.7139 (mtp180) REVERT: C 441 ASP cc_start: 0.8015 (m-30) cc_final: 0.7639 (m-30) REVERT: C 445 LYS cc_start: 0.7588 (mttt) cc_final: 0.7192 (mtpt) REVERT: C 449 ASP cc_start: 0.7674 (m-30) cc_final: 0.7385 (m-30) REVERT: C 483 ASN cc_start: 0.7279 (t0) cc_final: 0.6892 (m110) REVERT: D 34 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: E 5 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8050 (mm-40) REVERT: E 6 GLU cc_start: 0.7755 (mp0) cc_final: 0.7397 (mp0) REVERT: E 81 LYS cc_start: 0.8149 (mttp) cc_final: 0.7917 (mttp) REVERT: G 103 LYS cc_start: 0.7852 (ttmm) cc_final: 0.7303 (tptm) REVERT: H 6 GLU cc_start: 0.7868 (mp0) cc_final: 0.7457 (mp0) REVERT: H 34 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: H 105 GLN cc_start: 0.7563 (pm20) cc_final: 0.7192 (pm20) REVERT: L 70 THR cc_start: 0.8635 (m) cc_final: 0.8329 (m) outliers start: 52 outliers final: 36 residues processed: 260 average time/residue: 1.1271 time to fit residues: 332.0437 Evaluate side-chains 261 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 140 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 172 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 143 optimal weight: 0.0870 overall best weight: 0.8138 ------------------------------------------------------------------------------- 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** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN L 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107712 restraints weight = 19842.723| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.76 r_work: 0.3113 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17445 Z= 0.128 Angle : 0.521 7.944 23706 Z= 0.279 Chirality : 0.042 0.149 2595 Planarity : 0.003 0.031 3033 Dihedral : 5.964 88.169 2684 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.53 % Allowed : 14.38 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2121 helix: 2.91 (0.28), residues: 330 sheet: 0.52 (0.21), residues: 558 loop : -0.39 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 35A HIS 0.005 0.001 HIS B 471 PHE 0.024 0.002 PHE C 118 TYR 0.012 0.001 TYR E 102 ARG 0.006 0.000 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 12) link_NAG-ASN : angle 1.49637 ( 36) link_BETA1-4 : bond 0.00354 ( 3) link_BETA1-4 : angle 1.77237 ( 9) hydrogen bonds : bond 0.04059 ( 696) hydrogen bonds : angle 4.92963 ( 1944) link_BETA1-6 : bond 0.00365 ( 3) link_BETA1-6 : angle 1.06720 ( 9) SS BOND : bond 0.00207 ( 24) SS BOND : angle 1.93527 ( 48) covalent geometry : bond 0.00299 (17403) covalent geometry : angle 0.50996 (23604) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.6780 (pp20) REVERT: A 402 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8147 (mm) REVERT: A 404 ARG cc_start: 0.8264 (mmp-170) cc_final: 0.7961 (mmp-170) REVERT: A 413 MET cc_start: 0.8830 (ttp) cc_final: 0.8501 (ttp) REVERT: A 414 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7965 (mp0) REVERT: A 445 LYS cc_start: 0.7612 (mttt) cc_final: 0.7311 (mtmt) REVERT: A 483 ASN cc_start: 0.7641 (t0) cc_final: 0.7290 (m110) REVERT: A 490 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7767 (ttpp) REVERT: B 195 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: B 313 LYS cc_start: 0.8355 (ptmt) cc_final: 0.7653 (ptpt) REVERT: B 340 GLU cc_start: 0.7732 (mm-30) cc_final: 0.6447 (pp20) REVERT: B 402 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8171 (mm) REVERT: B 445 LYS cc_start: 0.7475 (mttt) cc_final: 0.7094 (mtpt) REVERT: B 460 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7572 (mtmt) REVERT: B 479 ASN cc_start: 0.7584 (m110) cc_final: 0.7302 (m-40) REVERT: C 64 CYS cc_start: 0.7166 (m) cc_final: 0.6784 (m) REVERT: C 137 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7594 (mpt180) REVERT: C 340 GLU cc_start: 0.8290 (mm-30) cc_final: 0.6456 (pp20) REVERT: C 344 GLN cc_start: 0.8691 (mt0) cc_final: 0.8381 (mt0) REVERT: C 432 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8164 (mm-30) REVERT: C 434 GLU cc_start: 0.8159 (tt0) cc_final: 0.7906 (tt0) REVERT: C 435 ARG cc_start: 0.7818 (mtm110) cc_final: 0.7070 (mtp180) REVERT: C 441 ASP cc_start: 0.7936 (m-30) cc_final: 0.7546 (m-30) REVERT: C 445 LYS cc_start: 0.7556 (mttt) cc_final: 0.7280 (mtmt) REVERT: C 449 ASP cc_start: 0.7674 (m-30) cc_final: 0.7390 (m-30) REVERT: C 483 ASN cc_start: 0.7270 (t0) cc_final: 0.6889 (m110) REVERT: D 34 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: E 5 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7883 (mm-40) REVERT: G 103 LYS cc_start: 0.7794 (ttmm) cc_final: 0.7279 (tptm) REVERT: H 2 VAL cc_start: 0.7587 (OUTLIER) cc_final: 0.7158 (p) REVERT: H 6 GLU cc_start: 0.7852 (mp0) cc_final: 0.7424 (mp0) REVERT: H 34 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: H 105 GLN cc_start: 0.7531 (pm20) cc_final: 0.7142 (pm20) REVERT: L 70 THR cc_start: 0.8595 (m) cc_final: 0.8295 (m) outliers start: 47 outliers final: 34 residues processed: 251 average time/residue: 1.1091 time to fit residues: 314.7856 Evaluate side-chains 261 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 107 optimal weight: 0.0970 chunk 162 optimal weight: 0.7980 chunk 175 optimal weight: 8.9990 chunk 44 optimal weight: 0.0010 chunk 53 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN L 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108791 restraints weight = 19885.814| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.76 r_work: 0.3129 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17445 Z= 0.110 Angle : 0.503 7.301 23706 Z= 0.269 Chirality : 0.041 0.141 2595 Planarity : 0.003 0.031 3033 Dihedral : 5.873 89.285 2684 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.37 % Allowed : 14.97 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2121 helix: 2.97 (0.28), residues: 330 sheet: 0.52 (0.21), residues: 564 loop : -0.33 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 35A HIS 0.005 0.001 HIS B 471 PHE 0.022 0.002 PHE B 118 TYR 0.011 0.001 TYR E 102 ARG 0.005 0.000 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 12) link_NAG-ASN : angle 1.43916 ( 36) link_BETA1-4 : bond 0.00335 ( 3) link_BETA1-4 : angle 1.70433 ( 9) hydrogen bonds : bond 0.03917 ( 696) hydrogen bonds : angle 4.86128 ( 1944) link_BETA1-6 : bond 0.00414 ( 3) link_BETA1-6 : angle 1.10808 ( 9) SS BOND : bond 0.00248 ( 24) SS BOND : angle 1.75924 ( 48) covalent geometry : bond 0.00251 (17403) covalent geometry : angle 0.49290 (23604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11930.03 seconds wall clock time: 206 minutes 26.66 seconds (12386.66 seconds total)