Starting phenix.real_space_refine on Sun Jun 15 06:56:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp7_41469/06_2025/8tp7_41469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp7_41469/06_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_41469/06_2025/8tp7_41469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp7_41469/06_2025/8tp7_41469.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp7_41469/06_2025/8tp7_41469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp7_41469/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.08, per 1000 atoms: 0.59 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: 4.47 Conformation dependent library (CDL) restraints added in 2.2 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: 2.97 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: 6.81 Time building geometry restraints manager: 5.23 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: 0.12 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 41.910 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.090 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:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.880 ------------------------------------------------------------------------------- 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 : 1.850 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: 1.4680 time to fit residues: 632.5881 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 : 2.039 ------------------------------------------------------------------------------- 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 = 0.138273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109480 restraints weight = 19258.311| |-----------------------------------------------------------------------------| 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 1.45108 ( 36) link_BETA1-4 : bond 0.00165 ( 3) link_BETA1-4 : angle 2.52624 ( 9) hydrogen bonds : bond 0.05375 ( 696) hydrogen bonds : angle 5.57115 ( 1944) link_BETA1-6 : bond 0.00856 ( 3) link_BETA1-6 : angle 0.97116 ( 9) SS BOND : bond 0.00252 ( 24) SS BOND : angle 1.34727 ( 48) covalent geometry : bond 0.00335 (17403) covalent geometry : angle 0.60889 (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 : 1.994 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: 0.8791 (t0) cc_final: 0.8484 (t0) REVERT: A 211 LYS cc_start: 0.8843 (tttp) cc_final: 0.7865 (tttm) REVERT: A 310 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8438 (mtmt) REVERT: A 340 GLU cc_start: 0.8600 (mm-30) cc_final: 0.6872 (pp20) REVERT: A 438 ASP cc_start: 0.8254 (m-30) cc_final: 0.7877 (m-30) REVERT: A 445 LYS cc_start: 0.7468 (mttt) cc_final: 0.7124 (mtpp) REVERT: B 88 MET cc_start: 0.8713 (mtp) cc_final: 0.8338 (mtp) REVERT: B 210 ASN cc_start: 0.8698 (t0) cc_final: 0.8324 (t0) REVERT: B 340 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6308 (pp20) REVERT: B 344 GLN cc_start: 0.8364 (mt0) cc_final: 0.7921 (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: 0.7651 (mttt) cc_final: 0.7245 (mtpt) REVERT: C 211 LYS cc_start: 0.8786 (tttp) cc_final: 0.8190 (tttm) REVERT: C 340 GLU cc_start: 0.8193 (mm-30) cc_final: 0.6672 (pp20) REVERT: C 344 GLN cc_start: 0.8452 (mt0) cc_final: 0.7920 (mt0) REVERT: C 434 GLU cc_start: 0.8108 (tt0) cc_final: 0.7870 (tt0) REVERT: C 435 ARG cc_start: 0.7846 (mtm110) cc_final: 0.7306 (mtt180) REVERT: C 438 ASP cc_start: 0.8098 (m-30) cc_final: 0.7657 (m-30) REVERT: C 445 LYS cc_start: 0.7609 (mttt) cc_final: 0.7008 (mtpp) REVERT: D 6 GLU cc_start: 0.7847 (mp0) cc_final: 0.7621 (mp0) REVERT: E 5 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8268 (mm-40) REVERT: H 6 GLU cc_start: 0.7721 (mp0) cc_final: 0.7339 (mp0) outliers start: 36 outliers final: 19 residues processed: 295 average time/residue: 1.6342 time to fit residues: 544.1629 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 : 2.074 ------------------------------------------------------------------------------- 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: 4.9990 chunk 198 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 0.0020 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: 0.1980 chunk 157 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 overall best weight: 1.2392 ------------------------------------------------------------------------------- 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 389 ASN C 391 GLN C 479 ASN E 5 GLN E 60 ASN E 77 GLN H 60 ASN H 77 GLN L 38 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107046 restraints weight = 19616.454| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.82 r_work: 0.3120 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17445 Z= 0.178 Angle : 0.581 8.900 23706 Z= 0.317 Chirality : 0.044 0.147 2595 Planarity : 0.004 0.036 3033 Dihedral : 6.514 85.436 2684 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.18 % Allowed : 10.72 % Favored : 86.11 % 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 (0.17), residues: 2121 helix: 2.51 (0.28), residues: 333 sheet: 0.69 (0.21), residues: 579 loop : -0.24 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 35A HIS 0.020 0.001 HIS C 471 PHE 0.029 0.002 PHE B 118 TYR 0.015 0.002 TYR H 102 ARG 0.003 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 12) link_NAG-ASN : angle 1.12803 ( 36) link_BETA1-4 : bond 0.00372 ( 3) link_BETA1-4 : angle 2.07200 ( 9) hydrogen bonds : bond 0.04865 ( 696) hydrogen bonds : angle 5.20545 ( 1944) link_BETA1-6 : bond 0.00548 ( 3) link_BETA1-6 : angle 1.02641 ( 9) SS BOND : bond 0.00811 ( 24) SS BOND : angle 1.14639 ( 48) covalent geometry : bond 0.00419 (17403) covalent geometry : angle 0.57693 (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 311 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 252 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8751 (mtp) cc_final: 0.8340 (mtp) REVERT: A 157 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8427 (tttt) REVERT: A 210 ASN cc_start: 0.8791 (t0) cc_final: 0.8529 (t0) REVERT: A 211 LYS cc_start: 0.8872 (tttp) cc_final: 0.8290 (tttm) REVERT: A 310 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8494 (mtmt) REVERT: A 340 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.6791 (pp20) REVERT: A 404 ARG cc_start: 0.8337 (mmp-170) cc_final: 0.8039 (mmp-170) REVERT: A 438 ASP cc_start: 0.8297 (m-30) cc_final: 0.7921 (m-30) REVERT: A 445 LYS cc_start: 0.7790 (mttt) cc_final: 0.7498 (mtmt) REVERT: A 490 LYS cc_start: 0.7457 (ttpt) cc_final: 0.7044 (ttmm) REVERT: B 210 ASN cc_start: 0.8745 (t0) cc_final: 0.8417 (t0) REVERT: B 340 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6435 (pp20) REVERT: B 402 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8166 (mm) REVERT: B 445 LYS cc_start: 0.7662 (mttt) cc_final: 0.7267 (mtpt) REVERT: B 460 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7565 (mtmt) REVERT: C 50 LYS cc_start: 0.7182 (mttt) cc_final: 0.6809 (mtmt) REVERT: C 211 LYS cc_start: 0.8760 (tttp) cc_final: 0.8169 (tttm) REVERT: C 340 GLU cc_start: 0.8277 (mm-30) cc_final: 0.6629 (pp20) REVERT: C 344 GLN cc_start: 0.8564 (mt0) cc_final: 0.8080 (mt0) REVERT: C 386 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7742 (mt-10) REVERT: C 404 ARG cc_start: 0.8425 (mmp-170) cc_final: 0.8128 (mmp-170) REVERT: C 432 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8230 (mm-30) REVERT: C 434 GLU cc_start: 0.8160 (tt0) cc_final: 0.7926 (tt0) REVERT: C 435 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7402 (mtt180) REVERT: C 438 ASP cc_start: 0.8183 (m-30) cc_final: 0.7846 (m-30) REVERT: C 441 ASP cc_start: 0.7955 (m-30) cc_final: 0.7688 (m-30) REVERT: C 445 LYS cc_start: 0.7592 (mttt) cc_final: 0.7068 (mtpp) REVERT: C 449 ASP cc_start: 0.7693 (m-30) cc_final: 0.7481 (m-30) REVERT: C 483 ASN cc_start: 0.7486 (t0) cc_final: 0.7029 (m110) REVERT: D 6 GLU cc_start: 0.8107 (mp0) cc_final: 0.7802 (mp0) REVERT: E 5 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8196 (mm-40) REVERT: H 6 GLU cc_start: 0.7805 (mp0) cc_final: 0.7423 (mp0) REVERT: H 105 GLN cc_start: 0.7603 (pm20) cc_final: 0.7320 (pm20) REVERT: L 74 SER cc_start: 0.8302 (t) cc_final: 0.7833 (m) outliers start: 59 outliers final: 33 residues processed: 285 average time/residue: 1.4442 time to fit residues: 463.8583 Evaluate side-chains 262 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 1.850 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 201 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN C 160 ASN E 5 GLN F 38 ASN G 38 ASN 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 = 0.3541 r_free = 0.3541 target = 0.133446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105496 restraints weight = 19740.672| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.80 r_work: 0.3095 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17445 Z= 0.196 Angle : 0.580 5.985 23706 Z= 0.312 Chirality : 0.044 0.141 2595 Planarity : 0.004 0.035 3033 Dihedral : 6.419 84.721 2684 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.34 % Allowed : 11.52 % Favored : 85.14 % 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: 2.55 (0.27), residues: 333 sheet: 0.48 (0.21), residues: 597 loop : -0.33 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 35A HIS 0.021 0.002 HIS B 471 PHE 0.029 0.002 PHE C 118 TYR 0.016 0.002 TYR D 100F ARG 0.003 0.000 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 12) link_NAG-ASN : angle 1.31027 ( 36) link_BETA1-4 : bond 0.00467 ( 3) link_BETA1-4 : angle 2.02637 ( 9) hydrogen bonds : bond 0.04737 ( 696) hydrogen bonds : angle 5.13405 ( 1944) link_BETA1-6 : bond 0.00563 ( 3) link_BETA1-6 : angle 1.02370 ( 9) SS BOND : bond 0.00250 ( 24) SS BOND : angle 1.18938 ( 48) covalent geometry : bond 0.00470 (17403) covalent geometry : angle 0.57477 (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 297 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 235 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 CYS cc_start: 0.7312 (m) cc_final: 0.6984 (m) REVERT: A 88 MET cc_start: 0.8772 (mtp) cc_final: 0.8334 (mtp) REVERT: A 157 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8466 (tttt) REVERT: A 210 ASN cc_start: 0.8807 (t0) cc_final: 0.8581 (t0) REVERT: A 211 LYS cc_start: 0.8867 (tttp) cc_final: 0.7923 (tttm) REVERT: A 310 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8481 (mtmt) REVERT: A 340 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.6832 (pp20) REVERT: A 404 ARG cc_start: 0.8361 (mmp-170) cc_final: 0.8067 (mmp-170) REVERT: A 414 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7989 (mp0) REVERT: A 445 LYS cc_start: 0.7728 (mttt) cc_final: 0.7465 (mtmt) REVERT: A 483 ASN cc_start: 0.7732 (t0) cc_final: 0.7280 (m110) REVERT: A 490 LYS cc_start: 0.7516 (ttpt) cc_final: 0.7159 (ttmm) REVERT: B 340 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6427 (pp20) REVERT: B 388 MET cc_start: 0.8717 (mmm) cc_final: 0.8463 (mmt) REVERT: B 402 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8165 (mm) REVERT: B 441 ASP cc_start: 0.8070 (m-30) cc_final: 0.7850 (m-30) REVERT: B 445 LYS cc_start: 0.7575 (mttt) cc_final: 0.7194 (mtpt) REVERT: B 460 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7567 (mtmt) REVERT: C 50 LYS cc_start: 0.7247 (mttt) cc_final: 0.6879 (mtmt) REVERT: C 137 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7528 (mpt180) REVERT: C 271 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: C 340 GLU cc_start: 0.8255 (mm-30) cc_final: 0.6527 (pp20) REVERT: C 432 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8273 (mm-30) REVERT: C 434 GLU cc_start: 0.8211 (tt0) cc_final: 0.7985 (tt0) REVERT: C 435 ARG cc_start: 0.7884 (mtm110) cc_final: 0.7156 (mtp180) REVERT: C 438 ASP cc_start: 0.8224 (m-30) cc_final: 0.7976 (m-30) REVERT: C 441 ASP cc_start: 0.8023 (m-30) cc_final: 0.7650 (m-30) REVERT: C 445 LYS cc_start: 0.7583 (mttt) cc_final: 0.7187 (mtpt) REVERT: C 449 ASP cc_start: 0.7681 (m-30) cc_final: 0.7399 (m-30) REVERT: C 483 ASN cc_start: 0.7478 (t0) cc_final: 0.6997 (m110) REVERT: D 3 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7769 (mt0) REVERT: E 5 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8076 (mm-40) REVERT: H 6 GLU cc_start: 0.7844 (mp0) cc_final: 0.7372 (mp0) REVERT: H 105 GLN cc_start: 0.7540 (pm20) cc_final: 0.7184 (pm20) REVERT: L 74 SER cc_start: 0.8279 (t) cc_final: 0.7825 (m) outliers start: 62 outliers final: 46 residues processed: 273 average time/residue: 1.1964 time to fit residues: 366.5446 Evaluate side-chains 274 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 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 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 462 LEU 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 159 SER Chi-restraints excluded: chain B residue 198 VAL 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 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 271 GLU 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 3 GLN 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 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=3.50 ------------------------------------------------------------------------------- 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: 2.9990 chunk 133 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN C 355 HIS E 5 GLN L 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.134992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107058 restraints weight = 19860.412| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.78 r_work: 0.3108 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17445 Z= 0.151 Angle : 0.529 5.726 23706 Z= 0.286 Chirality : 0.042 0.177 2595 Planarity : 0.004 0.033 3033 Dihedral : 6.243 84.881 2684 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.23 % Allowed : 12.55 % Favored : 84.22 % 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: 2.73 (0.28), residues: 333 sheet: 0.53 (0.21), residues: 591 loop : -0.36 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 35A HIS 0.011 0.001 HIS B 471 PHE 0.026 0.002 PHE A 118 TYR 0.012 0.002 TYR D 100F ARG 0.004 0.000 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 12) link_NAG-ASN : angle 1.34093 ( 36) link_BETA1-4 : bond 0.00397 ( 3) link_BETA1-4 : angle 1.88554 ( 9) hydrogen bonds : bond 0.04426 ( 696) hydrogen bonds : angle 4.98005 ( 1944) link_BETA1-6 : bond 0.00461 ( 3) link_BETA1-6 : angle 1.01730 ( 9) SS BOND : bond 0.00193 ( 24) SS BOND : angle 0.94524 ( 48) covalent geometry : bond 0.00358 (17403) covalent geometry : angle 0.52444 (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 294 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 234 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8751 (mtp) cc_final: 0.8404 (mtp) REVERT: A 211 LYS cc_start: 0.8899 (tttp) cc_final: 0.7954 (tttm) REVERT: A 310 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8435 (mtmt) REVERT: A 340 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.6776 (pp20) REVERT: A 402 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8079 (mm) REVERT: A 404 ARG cc_start: 0.8313 (mmp-170) cc_final: 0.7997 (mmp-170) REVERT: A 414 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8016 (mp0) REVERT: A 445 LYS cc_start: 0.7668 (mttt) cc_final: 0.7352 (mtmt) REVERT: A 483 ASN cc_start: 0.7744 (t0) cc_final: 0.7299 (m110) REVERT: A 490 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7242 (ttmm) REVERT: B 340 GLU cc_start: 0.7615 (mm-30) cc_final: 0.6388 (pp20) REVERT: B 402 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8120 (mm) REVERT: B 441 ASP cc_start: 0.7953 (m-30) cc_final: 0.7722 (m-30) REVERT: B 445 LYS cc_start: 0.7528 (mttt) cc_final: 0.7151 (mtpt) REVERT: B 460 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7506 (mtmt) REVERT: B 479 ASN cc_start: 0.7655 (m110) cc_final: 0.7391 (m-40) REVERT: C 50 LYS cc_start: 0.7285 (mttt) cc_final: 0.6845 (mtmt) REVERT: C 137 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7540 (mpt180) REVERT: C 340 GLU cc_start: 0.8235 (mm-30) cc_final: 0.6481 (pp20) REVERT: C 344 GLN cc_start: 0.8668 (mt0) cc_final: 0.8237 (mt0) REVERT: C 404 ARG cc_start: 0.8329 (mmp-170) cc_final: 0.8117 (mmp-170) REVERT: C 434 GLU cc_start: 0.8195 (tt0) cc_final: 0.7965 (tt0) REVERT: C 435 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7184 (mtp180) REVERT: C 438 ASP cc_start: 0.8237 (m-30) cc_final: 0.8021 (m-30) REVERT: C 441 ASP cc_start: 0.7948 (m-30) cc_final: 0.7553 (m-30) REVERT: C 445 LYS cc_start: 0.7544 (mttt) cc_final: 0.7158 (mtpt) REVERT: C 449 ASP cc_start: 0.7693 (m-30) cc_final: 0.7403 (m-30) REVERT: C 483 ASN cc_start: 0.7496 (t0) cc_final: 0.7011 (m110) REVERT: D 34 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: E 5 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8038 (mm-40) REVERT: H 6 GLU cc_start: 0.7789 (mp0) cc_final: 0.7438 (mp0) outliers start: 60 outliers final: 42 residues processed: 268 average time/residue: 1.2652 time to fit residues: 379.9620 Evaluate side-chains 267 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 427 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 198 VAL Chi-restraints excluded: chain B residue 213 SER 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 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 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 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: 0.8980 chunk 164 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 0.0370 chunk 5 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 169 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 183 optimal weight: 0.3980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS B 355 HIS E 5 GLN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.135769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108084 restraints weight = 19797.740| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.77 r_work: 0.3136 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17445 Z= 0.103 Angle : 0.478 5.065 23706 Z= 0.259 Chirality : 0.041 0.152 2595 Planarity : 0.003 0.031 3033 Dihedral : 5.957 85.693 2684 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.26 % Allowed : 13.73 % Favored : 84.01 % 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: 0.70 (0.18), residues: 2121 helix: 2.91 (0.28), residues: 333 sheet: 0.61 (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 0.021 0.001 PHE A 118 TYR 0.010 0.001 TYR D 35 ARG 0.004 0.000 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 12) link_NAG-ASN : angle 1.32256 ( 36) link_BETA1-4 : bond 0.00389 ( 3) link_BETA1-4 : angle 1.72524 ( 9) hydrogen bonds : bond 0.04022 ( 696) hydrogen bonds : angle 4.79862 ( 1944) link_BETA1-6 : bond 0.00447 ( 3) link_BETA1-6 : angle 1.08102 ( 9) SS BOND : bond 0.00189 ( 24) SS BOND : angle 0.78011 ( 48) covalent geometry : bond 0.00227 (17403) covalent geometry : angle 0.47295 (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 275 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8647 (mtp) cc_final: 0.8389 (mtp) REVERT: A 310 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8345 (mtmt) REVERT: A 340 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.6815 (pp20) REVERT: A 402 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8096 (mm) REVERT: A 404 ARG cc_start: 0.8288 (mmp-170) cc_final: 0.7974 (mmp-170) REVERT: A 414 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7923 (mp0) REVERT: A 445 LYS cc_start: 0.7593 (mttt) cc_final: 0.7284 (mtmt) REVERT: A 483 ASN cc_start: 0.7781 (t0) cc_final: 0.7374 (m110) REVERT: A 490 LYS cc_start: 0.7716 (ttpt) cc_final: 0.7487 (ttpp) REVERT: B 195 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: B 310 LYS cc_start: 0.8745 (mtmm) cc_final: 0.8512 (mtmt) REVERT: B 335 ILE cc_start: 0.6586 (tt) cc_final: 0.6374 (tt) REVERT: B 340 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6390 (pp20) REVERT: B 402 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8051 (mm) REVERT: B 445 LYS cc_start: 0.7422 (mttt) cc_final: 0.7045 (mtpt) REVERT: B 460 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7567 (mtmt) REVERT: B 479 ASN cc_start: 0.7529 (m110) cc_final: 0.7285 (m-40) REVERT: C 50 LYS cc_start: 0.7328 (mttt) cc_final: 0.6904 (mtmt) REVERT: C 137 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7539 (mpt180) REVERT: C 340 GLU cc_start: 0.8197 (mm-30) cc_final: 0.6472 (pp20) REVERT: C 344 GLN cc_start: 0.8681 (mt0) cc_final: 0.8245 (mm-40) REVERT: C 432 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8157 (mm-30) REVERT: C 434 GLU cc_start: 0.8140 (tt0) cc_final: 0.7921 (tt0) REVERT: C 435 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7084 (mtp180) REVERT: C 441 ASP cc_start: 0.7914 (m-30) cc_final: 0.7532 (m-30) REVERT: C 445 LYS cc_start: 0.7469 (mttt) cc_final: 0.7085 (mtpt) REVERT: C 449 ASP cc_start: 0.7653 (m-30) cc_final: 0.7368 (m-30) REVERT: C 483 ASN cc_start: 0.7484 (t0) cc_final: 0.7040 (m110) REVERT: D 34 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: E 5 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7895 (mm-40) REVERT: E 6 GLU cc_start: 0.7500 (mp0) cc_final: 0.7286 (mp0) REVERT: H 6 GLU cc_start: 0.7729 (mp0) cc_final: 0.7324 (mp0) REVERT: H 105 GLN cc_start: 0.7507 (pm20) cc_final: 0.7127 (pm20) outliers start: 42 outliers final: 20 residues processed: 257 average time/residue: 1.2375 time to fit residues: 355.7526 Evaluate side-chains 246 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 1.837 ------------------------------------------------------------------------------- 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 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 159 SER Chi-restraints excluded: chain B residue 195 TYR 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 23 THR 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 D residue 2 VAL Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain E residue 5 GLN 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 108 LEU Chi-restraints excluded: chain L residue 20 THR 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: 3.9990 chunk 147 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 145 optimal weight: 0.0870 chunk 152 optimal weight: 1.9990 chunk 209 optimal weight: 0.5980 overall best weight: 1.9364 ------------------------------------------------------------------------------- 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 L 53 HIS L 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.132624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104639 restraints weight = 19743.338| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.79 r_work: 0.3076 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17445 Z= 0.233 Angle : 0.601 6.601 23706 Z= 0.320 Chirality : 0.045 0.148 2595 Planarity : 0.004 0.043 3033 Dihedral : 6.260 85.114 2684 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.55 % Allowed : 12.92 % Favored : 83.52 % 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: 0.43 (0.18), residues: 2121 helix: 2.71 (0.27), residues: 330 sheet: 0.44 (0.21), residues: 555 loop : -0.45 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 103 HIS 0.006 0.001 HIS B 471 PHE 0.035 0.003 PHE C 118 TYR 0.020 0.002 TYR E 102 ARG 0.005 0.000 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 12) link_NAG-ASN : angle 1.52061 ( 36) link_BETA1-4 : bond 0.00433 ( 3) link_BETA1-4 : angle 2.06785 ( 9) hydrogen bonds : bond 0.04706 ( 696) hydrogen bonds : angle 5.06175 ( 1944) link_BETA1-6 : bond 0.00386 ( 3) link_BETA1-6 : angle 0.98413 ( 9) SS BOND : bond 0.00274 ( 24) SS BOND : angle 1.16125 ( 48) covalent geometry : bond 0.00570 (17403) covalent geometry : angle 0.59561 (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: 66 poor density : 234 time to evaluate : 1.889 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: 0.7238 (m) cc_final: 0.6864 (m) REVERT: A 88 MET cc_start: 0.8850 (mtp) cc_final: 0.8023 (ttm) REVERT: A 310 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8480 (mtmt) REVERT: A 340 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.6866 (pp20) REVERT: A 402 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8146 (mm) REVERT: A 404 ARG cc_start: 0.8317 (mmp-170) cc_final: 0.7984 (mmp-170) REVERT: A 414 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8050 (mp0) REVERT: A 445 LYS cc_start: 0.7817 (mttt) cc_final: 0.7507 (mtmt) REVERT: A 483 ASN cc_start: 0.7827 (t0) cc_final: 0.7350 (m110) REVERT: A 490 LYS cc_start: 0.7781 (ttpt) cc_final: 0.7494 (ttpp) REVERT: B 137 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8125 (mmt90) REVERT: B 195 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: B 340 GLU cc_start: 0.7757 (mm-30) cc_final: 0.6462 (pp20) REVERT: B 402 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8206 (mm) REVERT: B 441 ASP cc_start: 0.7986 (m-30) cc_final: 0.7784 (m-30) REVERT: B 445 LYS cc_start: 0.7552 (mttt) cc_final: 0.7200 (mtpt) REVERT: B 460 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7505 (mtmt) REVERT: B 479 ASN cc_start: 0.7686 (m110) cc_final: 0.7394 (m-40) REVERT: C 50 LYS cc_start: 0.7366 (mttt) cc_final: 0.6965 (mtpt) REVERT: C 137 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7549 (mpt180) REVERT: C 340 GLU cc_start: 0.8240 (mm-30) cc_final: 0.6534 (pp20) REVERT: C 432 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8213 (mm-30) REVERT: C 434 GLU cc_start: 0.8259 (tt0) cc_final: 0.8013 (tt0) REVERT: C 435 ARG cc_start: 0.7914 (mtm110) cc_final: 0.7234 (mtp180) REVERT: C 441 ASP cc_start: 0.8015 (m-30) cc_final: 0.7637 (m-30) REVERT: C 445 LYS cc_start: 0.7626 (mttt) cc_final: 0.7211 (mtpt) REVERT: C 449 ASP cc_start: 0.7693 (m-30) cc_final: 0.7380 (m-30) REVERT: C 483 ASN cc_start: 0.7488 (t0) cc_final: 0.7036 (m110) REVERT: D 34 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: E 5 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8084 (mm-40) REVERT: G 103 LYS cc_start: 0.7890 (ttmm) cc_final: 0.7302 (tptm) REVERT: H 6 GLU cc_start: 0.7805 (mp0) cc_final: 0.7465 (mp0) REVERT: H 34 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: H 70 SER cc_start: 0.8504 (t) cc_final: 0.8068 (m) REVERT: H 105 GLN cc_start: 0.7564 (pm20) cc_final: 0.7204 (pm20) outliers start: 66 outliers final: 45 residues processed: 274 average time/residue: 1.1566 time to fit residues: 357.6952 Evaluate side-chains 280 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 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 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 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 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 195 TYR 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 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 60 ASN 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: 0.3980 chunk 101 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.136099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108472 restraints weight = 19680.218| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.75 r_work: 0.3125 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17445 Z= 0.108 Angle : 0.493 9.529 23706 Z= 0.266 Chirality : 0.041 0.136 2595 Planarity : 0.003 0.031 3033 Dihedral : 5.950 86.908 2684 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.37 % Allowed : 14.22 % Favored : 83.41 % 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: 0.65 (0.18), residues: 2121 helix: 2.99 (0.28), residues: 330 sheet: 0.61 (0.21), residues: 558 loop : -0.36 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35A HIS 0.005 0.001 HIS B 471 PHE 0.019 0.001 PHE C 118 TYR 0.012 0.001 TYR E 102 ARG 0.004 0.000 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 12) link_NAG-ASN : angle 1.44604 ( 36) link_BETA1-4 : bond 0.00395 ( 3) link_BETA1-4 : angle 1.72866 ( 9) hydrogen bonds : bond 0.04035 ( 696) hydrogen bonds : angle 4.89565 ( 1944) link_BETA1-6 : bond 0.00441 ( 3) link_BETA1-6 : angle 1.08879 ( 9) SS BOND : bond 0.00226 ( 24) SS BOND : angle 1.58215 ( 48) covalent geometry : bond 0.00240 (17403) covalent geometry : angle 0.48413 (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 269 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8623 (mtpt) cc_final: 0.8364 (mtmt) REVERT: A 340 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.6780 (pp20) REVERT: A 402 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8151 (mm) REVERT: A 404 ARG cc_start: 0.8299 (mmp-170) cc_final: 0.7976 (mmp-170) REVERT: A 414 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7940 (mp0) REVERT: A 445 LYS cc_start: 0.7596 (mttt) cc_final: 0.7296 (mtmt) REVERT: A 483 ASN cc_start: 0.7783 (t0) cc_final: 0.7362 (m110) REVERT: A 490 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7690 (ttpp) REVERT: B 195 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: B 340 GLU cc_start: 0.7648 (mm-30) cc_final: 0.6377 (pp20) REVERT: B 402 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8131 (mm) REVERT: B 445 LYS cc_start: 0.7499 (mttt) cc_final: 0.7108 (mtpt) REVERT: B 460 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7554 (mtmt) REVERT: B 479 ASN cc_start: 0.7601 (m110) cc_final: 0.7316 (m-40) REVERT: C 50 LYS cc_start: 0.7373 (mttt) cc_final: 0.7103 (mtmp) REVERT: C 137 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7519 (mpt180) REVERT: C 340 GLU cc_start: 0.8240 (mm-30) cc_final: 0.6461 (pp20) REVERT: C 344 GLN cc_start: 0.8730 (mt0) cc_final: 0.8300 (mm-40) REVERT: C 432 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8244 (mm-30) REVERT: C 434 GLU cc_start: 0.8186 (tt0) cc_final: 0.7956 (tt0) REVERT: C 435 ARG cc_start: 0.7813 (mtm110) cc_final: 0.7173 (mtp180) REVERT: C 441 ASP cc_start: 0.7942 (m-30) cc_final: 0.7535 (m-30) REVERT: C 445 LYS cc_start: 0.7525 (mttt) cc_final: 0.7139 (mtpt) REVERT: C 449 ASP cc_start: 0.7647 (m-30) cc_final: 0.7364 (m-30) REVERT: C 483 ASN cc_start: 0.7447 (t0) cc_final: 0.7036 (m110) REVERT: D 34 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: E 5 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7849 (mm-40) REVERT: H 6 GLU cc_start: 0.7852 (mp0) cc_final: 0.7429 (mp0) REVERT: H 34 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: H 105 GLN cc_start: 0.7547 (pm20) cc_final: 0.7170 (pm20) REVERT: L 70 THR cc_start: 0.8635 (m) cc_final: 0.8329 (m) outliers start: 44 outliers final: 25 residues processed: 253 average time/residue: 1.1572 time to fit residues: 329.6179 Evaluate side-chains 250 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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 C residue 291 THR 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 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 H residue 25 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 84 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 47 optimal weight: 0.0270 chunk 151 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 183 optimal weight: 0.0670 overall best weight: 0.9978 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.134876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107291 restraints weight = 19872.362| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.77 r_work: 0.3107 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17445 Z= 0.142 Angle : 0.520 7.483 23706 Z= 0.277 Chirality : 0.042 0.140 2595 Planarity : 0.003 0.032 3033 Dihedral : 5.973 87.318 2684 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.42 % Allowed : 14.59 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.18), residues: 2121 helix: 2.93 (0.27), residues: 330 sheet: 0.58 (0.21), residues: 558 loop : -0.37 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 35A HIS 0.005 0.001 HIS B 471 PHE 0.026 0.002 PHE C 118 TYR 0.012 0.002 TYR E 102 ARG 0.004 0.000 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 12) link_NAG-ASN : angle 1.47157 ( 36) link_BETA1-4 : bond 0.00380 ( 3) link_BETA1-4 : angle 1.81423 ( 9) hydrogen bonds : bond 0.04151 ( 696) hydrogen bonds : angle 4.89459 ( 1944) link_BETA1-6 : bond 0.00387 ( 3) link_BETA1-6 : angle 1.07335 ( 9) SS BOND : bond 0.00183 ( 24) SS BOND : angle 1.42240 ( 48) covalent geometry : bond 0.00338 (17403) covalent geometry : angle 0.51189 (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 274 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8377 (mtmt) REVERT: A 340 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.6825 (pp20) REVERT: A 402 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8159 (mm) REVERT: A 404 ARG cc_start: 0.8264 (mmp-170) cc_final: 0.7958 (mmp-170) REVERT: A 414 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7956 (mp0) REVERT: A 445 LYS cc_start: 0.7616 (mttt) cc_final: 0.7305 (mtmt) REVERT: A 483 ASN cc_start: 0.7796 (t0) cc_final: 0.7343 (m110) REVERT: A 490 LYS cc_start: 0.7913 (ttpt) cc_final: 0.7662 (ttpp) REVERT: B 195 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: B 340 GLU cc_start: 0.7722 (mm-30) cc_final: 0.6459 (pp20) REVERT: B 402 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8109 (mm) REVERT: B 441 ASP cc_start: 0.8019 (m-30) cc_final: 0.7805 (m-30) REVERT: B 445 LYS cc_start: 0.7545 (mttt) cc_final: 0.7154 (mtpt) REVERT: B 460 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7509 (mtmt) REVERT: B 479 ASN cc_start: 0.7608 (m110) cc_final: 0.7329 (m-40) REVERT: C 50 LYS cc_start: 0.7429 (mttt) cc_final: 0.7228 (mtpm) REVERT: C 64 CYS cc_start: 0.7242 (m) cc_final: 0.6853 (m) REVERT: C 137 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7561 (mpt180) REVERT: C 340 GLU cc_start: 0.8217 (mm-30) cc_final: 0.6491 (pp20) REVERT: C 344 GLN cc_start: 0.8774 (mt0) cc_final: 0.8339 (mm-40) REVERT: C 432 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8268 (mm-30) REVERT: C 434 GLU cc_start: 0.8168 (tt0) cc_final: 0.7923 (tt0) REVERT: C 435 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7243 (mtp180) REVERT: C 441 ASP cc_start: 0.7948 (m-30) cc_final: 0.7555 (m-30) REVERT: C 445 LYS cc_start: 0.7572 (mttt) cc_final: 0.7176 (mtpt) REVERT: C 449 ASP cc_start: 0.7654 (m-30) cc_final: 0.7367 (m-30) REVERT: C 483 ASN cc_start: 0.7451 (t0) cc_final: 0.7016 (m110) REVERT: D 34 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: E 5 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8045 (mm-40) REVERT: G 60 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7667 (m-40) REVERT: H 6 GLU cc_start: 0.7857 (mp0) cc_final: 0.7432 (mp0) REVERT: H 34 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: H 105 GLN cc_start: 0.7553 (pm20) cc_final: 0.7176 (pm20) REVERT: L 70 THR cc_start: 0.8634 (m) cc_final: 0.8329 (m) outliers start: 45 outliers final: 31 residues processed: 259 average time/residue: 1.1880 time to fit residues: 347.0185 Evaluate side-chains 257 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 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 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 340 GLU Chi-restraints excluded: chain A residue 378 THR 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 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 291 THR 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 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 F residue 85 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain H residue 25 SER 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: 0.0170 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- 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** B 483 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106956 restraints weight = 19827.206| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.77 r_work: 0.3103 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17445 Z= 0.153 Angle : 0.536 7.838 23706 Z= 0.285 Chirality : 0.043 0.230 2595 Planarity : 0.004 0.032 3033 Dihedral : 6.021 87.667 2684 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.69 % Allowed : 14.59 % Favored : 82.71 % 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: 2.88 (0.27), residues: 330 sheet: 0.54 (0.21), residues: 558 loop : -0.39 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35A HIS 0.004 0.001 HIS B 471 PHE 0.026 0.002 PHE C 118 TYR 0.013 0.002 TYR E 102 ARG 0.007 0.000 ARG B 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 12) link_NAG-ASN : angle 1.66250 ( 36) link_BETA1-4 : bond 0.00412 ( 3) link_BETA1-4 : angle 1.81541 ( 9) hydrogen bonds : bond 0.04196 ( 696) hydrogen bonds : angle 4.89802 ( 1944) link_BETA1-6 : bond 0.00379 ( 3) link_BETA1-6 : angle 1.06844 ( 9) SS BOND : bond 0.00218 ( 24) SS BOND : angle 1.58207 ( 48) covalent geometry : bond 0.00364 (17403) covalent geometry : angle 0.52671 (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 272 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8378 (mtmt) REVERT: A 340 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.6829 (pp20) REVERT: A 402 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8193 (mm) REVERT: A 404 ARG cc_start: 0.8277 (mmp-170) cc_final: 0.7975 (mmp-170) REVERT: A 414 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7946 (mp0) REVERT: A 445 LYS cc_start: 0.7643 (mttt) cc_final: 0.7326 (mtmt) REVERT: A 483 ASN cc_start: 0.7648 (t0) cc_final: 0.7296 (m110) REVERT: A 490 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7667 (ttpp) REVERT: B 137 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8110 (mmt90) REVERT: B 195 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: B 340 GLU cc_start: 0.7760 (mm-30) cc_final: 0.6466 (pp20) REVERT: B 388 MET cc_start: 0.8727 (mmm) cc_final: 0.8517 (mmm) REVERT: B 402 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8116 (mm) REVERT: B 445 LYS cc_start: 0.7541 (mttt) cc_final: 0.7145 (mtpt) REVERT: B 460 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7504 (mtmt) REVERT: B 479 ASN cc_start: 0.7636 (m110) cc_final: 0.7330 (m-40) REVERT: C 64 CYS cc_start: 0.7252 (m) cc_final: 0.6876 (m) REVERT: C 137 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7566 (mpt180) REVERT: C 340 GLU cc_start: 0.8215 (mm-30) cc_final: 0.6500 (pp20) REVERT: C 344 GLN cc_start: 0.8779 (mt0) cc_final: 0.8403 (mt0) REVERT: C 432 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8169 (mm-30) REVERT: C 434 GLU cc_start: 0.8165 (tt0) cc_final: 0.7918 (tt0) REVERT: C 435 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7239 (mtp180) REVERT: C 441 ASP cc_start: 0.7966 (m-30) cc_final: 0.7577 (m-30) REVERT: C 445 LYS cc_start: 0.7567 (mttt) cc_final: 0.7282 (mtmt) REVERT: C 449 ASP cc_start: 0.7681 (m-30) cc_final: 0.7398 (m-30) REVERT: C 483 ASN cc_start: 0.7276 (t0) cc_final: 0.6877 (m110) REVERT: D 34 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: E 5 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8031 (mm-40) REVERT: G 60 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7534 (m-40) REVERT: G 103 LYS cc_start: 0.7849 (ttmm) cc_final: 0.7300 (tptm) REVERT: H 2 VAL cc_start: 0.7649 (OUTLIER) cc_final: 0.7244 (p) REVERT: H 6 GLU cc_start: 0.7887 (mp0) cc_final: 0.7473 (mp0) REVERT: H 34 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: H 105 GLN cc_start: 0.7559 (pm20) cc_final: 0.7182 (pm20) REVERT: L 70 THR cc_start: 0.8607 (m) cc_final: 0.8309 (m) outliers start: 50 outliers final: 34 residues processed: 252 average time/residue: 1.1140 time to fit residues: 317.8287 Evaluate side-chains 263 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 93 ARG 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 340 GLU Chi-restraints excluded: chain A residue 378 THR 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 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 291 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 137 ARG Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 291 THR 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 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 20 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER 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: 0.8980 chunk 186 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 175 optimal weight: 8.9990 chunk 44 optimal weight: 0.0020 chunk 53 optimal weight: 2.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.134751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107224 restraints weight = 19941.751| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.78 r_work: 0.3120 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17445 Z= 0.116 Angle : 0.507 6.725 23706 Z= 0.272 Chirality : 0.042 0.234 2595 Planarity : 0.003 0.031 3033 Dihedral : 5.933 88.624 2684 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.48 % Allowed : 14.92 % Favored : 82.61 % 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: 0.65 (0.18), residues: 2121 helix: 2.95 (0.27), residues: 330 sheet: 0.59 (0.21), residues: 558 loop : -0.34 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 35A HIS 0.004 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 0.00169 ( 12) link_NAG-ASN : angle 1.63432 ( 36) link_BETA1-4 : bond 0.00343 ( 3) link_BETA1-4 : angle 1.72214 ( 9) hydrogen bonds : bond 0.03994 ( 696) hydrogen bonds : angle 4.83412 ( 1944) link_BETA1-6 : bond 0.00406 ( 3) link_BETA1-6 : angle 1.10006 ( 9) SS BOND : bond 0.00236 ( 24) SS BOND : angle 1.38772 ( 48) covalent geometry : bond 0.00266 (17403) covalent geometry : angle 0.49849 (23604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13155.75 seconds wall clock time: 229 minutes 8.61 seconds (13748.61 seconds total)