Starting phenix.real_space_refine on Sun Aug 24 04:43:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp7_41469/08_2025/8tp7_41469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp7_41469/08_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_41469/08_2025/8tp7_41469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp7_41469/08_2025/8tp7_41469.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp7_41469/08_2025/8tp7_41469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp7_41469/08_2025/8tp7_41469.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.077 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.82, per 1000 atoms: 0.28 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: 1.84 Conformation dependent library (CDL) restraints added in 804.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.88 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: 3.94 Time building geometry restraints manager: 2.34 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.930 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.920 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (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 ARG 0.007 0.001 ARG A 93 TYR 0.068 0.010 TYR A 195 PHE 0.051 0.006 PHE C 118 TRP 0.035 0.009 TRP L 35 HIS 0.006 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.02090 (17403) covalent geometry : angle 1.79510 (23604) SS BOND : bond 0.01390 ( 24) SS BOND : angle 2.84419 ( 48) hydrogen bonds : bond 0.13533 ( 696) hydrogen bonds : angle 7.28754 ( 1944) link_BETA1-4 : bond 0.07505 ( 3) link_BETA1-4 : angle 5.11669 ( 9) link_BETA1-6 : bond 0.05522 ( 3) link_BETA1-6 : angle 2.35665 ( 9) link_NAG-ASN : bond 0.07781 ( 12) link_NAG-ASN : angle 2.00693 ( 36) *********************** 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 : 0.766 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: 0.6649 time to fit residues: 285.8039 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 : 0.571 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 D 60 ASN E 5 GLN 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108493 restraints weight = 19212.627| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.79 r_work: 0.3114 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17445 Z= 0.160 Angle : 0.622 5.777 23706 Z= 0.345 Chirality : 0.044 0.185 2595 Planarity : 0.004 0.033 3033 Dihedral : 6.933 86.118 2686 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.15 % Allowed : 8.56 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.17), residues: 2121 helix: 2.39 (0.28), residues: 333 sheet: 0.94 (0.22), residues: 543 loop : -0.18 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 32 TYR 0.018 0.002 TYR E 35 PHE 0.027 0.002 PHE B 118 TRP 0.021 0.002 TRP E 35A HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00355 (17403) covalent geometry : angle 0.61605 (23604) SS BOND : bond 0.00333 ( 24) SS BOND : angle 1.36790 ( 48) hydrogen bonds : bond 0.05435 ( 696) hydrogen bonds : angle 5.58711 ( 1944) link_BETA1-4 : bond 0.00206 ( 3) link_BETA1-4 : angle 2.57819 ( 9) link_BETA1-6 : bond 0.01200 ( 3) link_BETA1-6 : angle 0.97094 ( 9) link_NAG-ASN : bond 0.00158 ( 12) link_NAG-ASN : angle 1.38864 ( 36) *********************** 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 318 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 278 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8824 (mtp) cc_final: 0.8288 (mtp) REVERT: A 210 ASN cc_start: 0.8774 (t0) cc_final: 0.8476 (t0) REVERT: A 211 LYS cc_start: 0.8849 (tttp) cc_final: 0.7870 (tttm) REVERT: A 310 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8440 (mtmt) REVERT: A 340 GLU cc_start: 0.8621 (mm-30) cc_final: 0.6899 (pp20) REVERT: A 344 GLN cc_start: 0.8479 (mt0) cc_final: 0.7862 (mt0) REVERT: A 438 ASP cc_start: 0.8260 (m-30) cc_final: 0.7883 (m-30) REVERT: A 445 LYS cc_start: 0.7497 (mttt) cc_final: 0.7165 (mtpp) REVERT: B 88 MET cc_start: 0.8737 (mtp) cc_final: 0.8356 (mtp) REVERT: B 210 ASN cc_start: 0.8698 (t0) cc_final: 0.8327 (t0) REVERT: B 340 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6261 (pp20) REVERT: B 402 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7994 (mm) REVERT: B 438 ASP cc_start: 0.8190 (m-30) cc_final: 0.7866 (m-30) REVERT: B 445 LYS cc_start: 0.7644 (mttt) cc_final: 0.7236 (mtpt) REVERT: C 211 LYS cc_start: 0.8792 (tttp) cc_final: 0.8195 (tttm) REVERT: C 340 GLU cc_start: 0.8216 (mm-30) cc_final: 0.6665 (pp20) REVERT: C 344 GLN cc_start: 0.8455 (mt0) cc_final: 0.7931 (mt0) REVERT: C 372 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7466 (ttpt) REVERT: C 434 GLU cc_start: 0.8120 (tt0) cc_final: 0.7869 (tt0) REVERT: C 435 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7320 (mtt180) REVERT: C 438 ASP cc_start: 0.8215 (m-30) cc_final: 0.7803 (m-30) REVERT: C 445 LYS cc_start: 0.7626 (mttt) cc_final: 0.7026 (mtpp) REVERT: E 5 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8234 (mm-40) REVERT: H 6 GLU cc_start: 0.7742 (mp0) cc_final: 0.7410 (mp0) outliers start: 40 outliers final: 21 residues processed: 296 average time/residue: 0.5851 time to fit residues: 195.0166 Evaluate side-chains 245 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 142 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 372 LYS 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 F residue 85 ASP 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 145 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 0.0070 chunk 170 optimal weight: 6.9990 chunk 100 optimal weight: 0.0370 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 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 77 GLN F 38 ASN H 77 GLN L 38 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107330 restraints weight = 19873.563| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.83 r_work: 0.3107 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17445 Z= 0.192 Angle : 0.596 5.982 23706 Z= 0.325 Chirality : 0.044 0.142 2595 Planarity : 0.004 0.037 3033 Dihedral : 6.579 85.107 2684 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.96 % Allowed : 10.88 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.17), residues: 2121 helix: 2.46 (0.28), residues: 333 sheet: 0.66 (0.20), residues: 594 loop : -0.29 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 435 TYR 0.015 0.002 TYR E 35 PHE 0.030 0.003 PHE B 118 TRP 0.018 0.002 TRP E 35A HIS 0.021 0.002 HIS C 471 Details of bonding type rmsd covalent geometry : bond 0.00456 (17403) covalent geometry : angle 0.59133 (23604) SS BOND : bond 0.00606 ( 24) SS BOND : angle 1.16760 ( 48) hydrogen bonds : bond 0.04953 ( 696) hydrogen bonds : angle 5.23207 ( 1944) link_BETA1-4 : bond 0.00483 ( 3) link_BETA1-4 : angle 2.06586 ( 9) link_BETA1-6 : bond 0.00559 ( 3) link_BETA1-6 : angle 0.94138 ( 9) link_NAG-ASN : bond 0.00246 ( 12) link_NAG-ASN : angle 1.12772 ( 36) *********************** 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 309 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8766 (mtp) cc_final: 0.8321 (mtp) REVERT: A 157 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8482 (tttt) REVERT: A 210 ASN cc_start: 0.8809 (t0) cc_final: 0.8549 (t0) REVERT: A 211 LYS cc_start: 0.8888 (tttp) cc_final: 0.7959 (tttm) REVERT: A 310 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8498 (mtmt) REVERT: A 340 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.6842 (pp20) REVERT: A 404 ARG cc_start: 0.8343 (mmp-170) cc_final: 0.8059 (mmp-170) REVERT: A 438 ASP cc_start: 0.8323 (m-30) cc_final: 0.7946 (m-30) REVERT: A 445 LYS cc_start: 0.7795 (mttt) cc_final: 0.7514 (mtmt) REVERT: A 490 LYS cc_start: 0.7467 (ttpt) cc_final: 0.7072 (ttmm) REVERT: B 210 ASN cc_start: 0.8758 (t0) cc_final: 0.8430 (t0) REVERT: B 340 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6415 (pp20) REVERT: B 344 GLN cc_start: 0.8752 (mt0) cc_final: 0.8158 (mm-40) REVERT: B 402 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8142 (mm) REVERT: B 441 ASP cc_start: 0.7951 (m-30) cc_final: 0.7719 (m-30) REVERT: B 445 LYS cc_start: 0.7663 (mttt) cc_final: 0.7267 (mtpt) REVERT: B 460 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7545 (mtmt) REVERT: C 50 LYS cc_start: 0.7188 (mttt) cc_final: 0.6807 (mtmt) REVERT: C 211 LYS cc_start: 0.8812 (tttp) cc_final: 0.8216 (tttm) REVERT: C 340 GLU cc_start: 0.8245 (mm-30) cc_final: 0.6629 (pp20) REVERT: C 344 GLN cc_start: 0.8583 (mt0) cc_final: 0.8104 (mt0) REVERT: C 372 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7524 (ttpt) REVERT: C 386 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7737 (mt-10) REVERT: C 404 ARG cc_start: 0.8406 (mmp-170) cc_final: 0.8150 (mmp-170) REVERT: C 434 GLU cc_start: 0.8181 (tt0) cc_final: 0.7942 (tt0) REVERT: C 438 ASP cc_start: 0.8200 (m-30) cc_final: 0.7874 (m-30) REVERT: C 441 ASP cc_start: 0.8012 (m-30) cc_final: 0.7738 (m-30) REVERT: C 445 LYS cc_start: 0.7608 (mttt) cc_final: 0.7084 (mtpp) REVERT: C 483 ASN cc_start: 0.7518 (t0) cc_final: 0.7038 (m110) REVERT: D 6 GLU cc_start: 0.7929 (mp0) cc_final: 0.7690 (mp0) REVERT: E 5 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8115 (mm-40) REVERT: H 6 GLU cc_start: 0.7821 (mp0) cc_final: 0.7426 (mp0) REVERT: H 105 GLN cc_start: 0.7614 (pm20) cc_final: 0.7329 (pm20) REVERT: L 74 SER cc_start: 0.8306 (t) cc_final: 0.7836 (m) outliers start: 55 outliers final: 36 residues processed: 283 average time/residue: 0.5701 time to fit residues: 180.9747 Evaluate side-chains 266 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 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 372 LYS Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 E 60 ASN G 38 ASN H 60 ASN H 77 GLN L 53 HIS L 69 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104959 restraints weight = 19776.470| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.82 r_work: 0.3077 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17445 Z= 0.234 Angle : 0.620 6.351 23706 Z= 0.333 Chirality : 0.045 0.148 2595 Planarity : 0.004 0.042 3033 Dihedral : 6.532 84.222 2684 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.72 % Allowed : 11.36 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.18), residues: 2121 helix: 2.42 (0.27), residues: 333 sheet: 0.42 (0.21), residues: 594 loop : -0.41 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 435 TYR 0.018 0.002 TYR D 100F PHE 0.031 0.003 PHE A 118 TRP 0.016 0.002 TRP H 35A HIS 0.017 0.002 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00569 (17403) covalent geometry : angle 0.61395 (23604) SS BOND : bond 0.00306 ( 24) SS BOND : angle 1.32860 ( 48) hydrogen bonds : bond 0.04940 ( 696) hydrogen bonds : angle 5.20385 ( 1944) link_BETA1-4 : bond 0.00403 ( 3) link_BETA1-4 : angle 2.17048 ( 9) link_BETA1-6 : bond 0.00483 ( 3) link_BETA1-6 : angle 0.96548 ( 9) link_NAG-ASN : bond 0.00169 ( 12) link_NAG-ASN : angle 1.38290 ( 36) *********************** 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 306 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 237 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8842 (mtp) cc_final: 0.8388 (mtp) REVERT: A 210 ASN cc_start: 0.8807 (t0) cc_final: 0.8600 (t0) REVERT: A 211 LYS cc_start: 0.8874 (tttp) cc_final: 0.7903 (tttm) REVERT: A 310 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8484 (mtmt) REVERT: A 340 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.6808 (pp20) REVERT: A 404 ARG cc_start: 0.8355 (mmp-170) cc_final: 0.8061 (mmp-170) REVERT: A 445 LYS cc_start: 0.7714 (mttt) cc_final: 0.7438 (mtmt) REVERT: A 483 ASN cc_start: 0.7782 (t0) cc_final: 0.7292 (m110) REVERT: A 490 LYS cc_start: 0.7571 (ttpt) cc_final: 0.7218 (ttmm) REVERT: B 340 GLU cc_start: 0.7658 (mm-30) cc_final: 0.6489 (pp20) REVERT: B 344 GLN cc_start: 0.8705 (mt0) cc_final: 0.8295 (mm-40) REVERT: B 402 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8194 (mm) REVERT: B 445 LYS cc_start: 0.7585 (mttt) cc_final: 0.7201 (mtpt) REVERT: B 460 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7647 (mtmt) REVERT: C 50 LYS cc_start: 0.7383 (mttt) cc_final: 0.6983 (mtmt) REVERT: C 137 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7543 (mpt180) REVERT: C 340 GLU cc_start: 0.8329 (mm-30) cc_final: 0.6518 (pp20) REVERT: C 344 GLN cc_start: 0.8636 (mt0) cc_final: 0.8200 (mt0) REVERT: C 372 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7519 (ttpt) REVERT: C 432 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8253 (mm-30) REVERT: C 434 GLU cc_start: 0.8250 (tt0) cc_final: 0.8025 (tt0) REVERT: C 435 ARG cc_start: 0.7934 (mtm110) cc_final: 0.7122 (mtp180) REVERT: C 441 ASP cc_start: 0.8063 (m-30) cc_final: 0.7677 (m-30) REVERT: C 445 LYS cc_start: 0.7531 (mttt) cc_final: 0.7156 (mtpt) REVERT: C 483 ASN cc_start: 0.7528 (t0) cc_final: 0.7030 (m110) REVERT: D 3 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: D 34 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: E 5 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8255 (mm-40) REVERT: H 6 GLU cc_start: 0.7854 (mp0) cc_final: 0.7391 (mp0) REVERT: H 105 GLN cc_start: 0.7531 (pm20) cc_final: 0.7188 (pm20) REVERT: L 74 SER cc_start: 0.8268 (t) cc_final: 0.7794 (m) outliers start: 69 outliers final: 47 residues processed: 273 average time/residue: 0.5709 time to fit residues: 174.2714 Evaluate side-chains 272 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 217 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 93 ARG Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 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 273 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 372 LYS 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 34 TYR 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 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 6 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 HIS B 389 ASN C 355 HIS E 5 GLN L 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106486 restraints weight = 19653.608| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.80 r_work: 0.3110 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3255 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= 0.130 Angle : 0.516 5.511 23706 Z= 0.279 Chirality : 0.042 0.146 2595 Planarity : 0.003 0.032 3033 Dihedral : 6.203 85.250 2684 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.58 % Allowed : 13.25 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.18), residues: 2121 helix: 2.76 (0.28), residues: 333 sheet: 0.49 (0.20), residues: 606 loop : -0.36 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 435 TYR 0.011 0.001 TYR D 100F PHE 0.024 0.002 PHE A 118 TRP 0.013 0.001 TRP H 35A HIS 0.010 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00299 (17403) covalent geometry : angle 0.51077 (23604) SS BOND : bond 0.00354 ( 24) SS BOND : angle 0.97178 ( 48) hydrogen bonds : bond 0.04332 ( 696) hydrogen bonds : angle 4.96508 ( 1944) link_BETA1-4 : bond 0.00380 ( 3) link_BETA1-4 : angle 1.84322 ( 9) link_BETA1-6 : bond 0.00466 ( 3) link_BETA1-6 : angle 1.04470 ( 9) link_NAG-ASN : bond 0.00187 ( 12) link_NAG-ASN : angle 1.37076 ( 36) *********************** 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 284 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 0.747 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: 0.8754 (mtp) cc_final: 0.8423 (mtp) REVERT: A 211 LYS cc_start: 0.8911 (tttp) cc_final: 0.7967 (tttm) REVERT: A 310 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8353 (mtmt) REVERT: A 340 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.6805 (pp20) REVERT: A 402 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8078 (mm) REVERT: A 404 ARG cc_start: 0.8340 (mmp-170) cc_final: 0.8032 (mmp-170) REVERT: A 445 LYS cc_start: 0.7615 (mttt) cc_final: 0.7307 (mtmt) REVERT: A 483 ASN cc_start: 0.7784 (t0) cc_final: 0.7332 (m110) REVERT: A 490 LYS cc_start: 0.7747 (ttpt) cc_final: 0.7489 (ttpp) REVERT: B 195 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: B 340 GLU cc_start: 0.7645 (mm-30) cc_final: 0.6411 (pp20) REVERT: B 402 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8180 (mm) REVERT: B 445 LYS cc_start: 0.7512 (mttt) cc_final: 0.7143 (mtpt) REVERT: B 460 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7732 (mtmt) REVERT: B 479 ASN cc_start: 0.7654 (m110) cc_final: 0.7386 (m-40) REVERT: C 50 LYS cc_start: 0.7347 (mttt) cc_final: 0.6934 (mtmt) REVERT: C 137 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7541 (mpt180) REVERT: C 340 GLU cc_start: 0.8195 (mm-30) cc_final: 0.6459 (pp20) REVERT: C 372 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7492 (ttpt) REVERT: C 434 GLU cc_start: 0.8207 (tt0) cc_final: 0.7960 (tt0) REVERT: C 435 ARG cc_start: 0.7889 (mtm110) cc_final: 0.7144 (mtp180) REVERT: C 441 ASP cc_start: 0.8020 (m-30) cc_final: 0.7618 (m-30) REVERT: C 445 LYS cc_start: 0.7478 (mttt) cc_final: 0.7101 (mtpt) REVERT: C 483 ASN cc_start: 0.7551 (t0) cc_final: 0.7057 (m110) REVERT: E 5 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8017 (mm-40) REVERT: E 6 GLU cc_start: 0.7760 (mp0) cc_final: 0.7522 (mp0) REVERT: H 6 GLU cc_start: 0.7799 (mp0) cc_final: 0.7396 (mp0) REVERT: H 70 SER cc_start: 0.8479 (t) cc_final: 0.8102 (m) REVERT: H 105 GLN cc_start: 0.7493 (pm20) cc_final: 0.7050 (pm20) outliers start: 48 outliers final: 28 residues processed: 264 average time/residue: 0.6196 time to fit residues: 183.1826 Evaluate side-chains 255 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 340 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 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 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 372 LYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 25 SER 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 20 THR 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 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 Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 190 optimal weight: 0.3980 chunk 172 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 0.0030 chunk 146 optimal weight: 0.7980 chunk 205 optimal weight: 0.0670 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS E 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108417 restraints weight = 19771.692| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.80 r_work: 0.3138 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17445 Z= 0.098 Angle : 0.473 4.889 23706 Z= 0.257 Chirality : 0.040 0.159 2595 Planarity : 0.003 0.030 3033 Dihedral : 5.919 86.352 2684 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.48 % Allowed : 13.89 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.18), residues: 2121 helix: 2.90 (0.28), residues: 333 sheet: 0.63 (0.21), residues: 576 loop : -0.30 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 137 TYR 0.010 0.001 TYR D 35 PHE 0.020 0.001 PHE A 118 TRP 0.012 0.001 TRP H 35A HIS 0.006 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00212 (17403) covalent geometry : angle 0.46806 (23604) SS BOND : bond 0.00166 ( 24) SS BOND : angle 0.86463 ( 48) hydrogen bonds : bond 0.03972 ( 696) hydrogen bonds : angle 4.75983 ( 1944) link_BETA1-4 : bond 0.00427 ( 3) link_BETA1-4 : angle 1.72020 ( 9) link_BETA1-6 : bond 0.00454 ( 3) link_BETA1-6 : angle 1.10155 ( 9) link_NAG-ASN : bond 0.00143 ( 12) link_NAG-ASN : angle 1.33134 ( 36) *********************** 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 286 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8656 (mtp) cc_final: 0.8406 (mtp) REVERT: A 310 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8338 (mtmt) REVERT: A 340 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.6773 (pp20) REVERT: A 402 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8083 (mm) REVERT: A 404 ARG cc_start: 0.8276 (mmp-170) cc_final: 0.7977 (mmp-170) REVERT: A 445 LYS cc_start: 0.7560 (mttt) cc_final: 0.7259 (mtmt) REVERT: A 483 ASN cc_start: 0.7752 (t0) cc_final: 0.7320 (m110) REVERT: A 490 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7542 (ttpt) REVERT: B 195 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: B 310 LYS cc_start: 0.8745 (mtmm) cc_final: 0.8495 (mtmt) REVERT: B 335 ILE cc_start: 0.6393 (tt) cc_final: 0.6189 (tt) REVERT: B 340 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6273 (pp20) REVERT: B 402 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8102 (mm) REVERT: B 445 LYS cc_start: 0.7416 (mttt) cc_final: 0.7137 (mtpt) REVERT: B 479 ASN cc_start: 0.7594 (m110) cc_final: 0.7310 (m-40) REVERT: C 50 LYS cc_start: 0.7384 (mttt) cc_final: 0.6928 (mtmt) REVERT: C 137 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7496 (mpt180) REVERT: C 340 GLU cc_start: 0.8213 (mm-30) cc_final: 0.6430 (pp20) REVERT: C 344 GLN cc_start: 0.8808 (mt0) cc_final: 0.8491 (mm-40) REVERT: C 432 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8169 (mm-30) REVERT: C 434 GLU cc_start: 0.8116 (tt0) cc_final: 0.7887 (tt0) REVERT: C 435 ARG cc_start: 0.7804 (mtm110) cc_final: 0.7032 (mtp180) REVERT: C 441 ASP cc_start: 0.7931 (m-30) cc_final: 0.7548 (m-30) REVERT: C 445 LYS cc_start: 0.7402 (mttt) cc_final: 0.7025 (mtpt) REVERT: C 483 ASN cc_start: 0.7499 (t0) cc_final: 0.7012 (m110) REVERT: D 34 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: E 5 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8026 (mm-40) REVERT: E 6 GLU cc_start: 0.7675 (mp0) cc_final: 0.7392 (mp0) REVERT: E 81 LYS cc_start: 0.8031 (mttp) cc_final: 0.7813 (mttm) REVERT: H 6 GLU cc_start: 0.7793 (mp0) cc_final: 0.7341 (mp0) REVERT: H 34 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: H 105 GLN cc_start: 0.7443 (pm20) cc_final: 0.7032 (pm20) outliers start: 46 outliers final: 22 residues processed: 265 average time/residue: 0.6407 time to fit residues: 189.8932 Evaluate side-chains 243 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 A residue 490 LYS Chi-restraints excluded: chain B residue 23 THR 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 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 195 TYR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 78 VAL 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 181 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 188 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN L 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.102703 restraints weight = 19924.146| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.80 r_work: 0.3053 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 17445 Z= 0.310 Angle : 0.680 7.453 23706 Z= 0.358 Chirality : 0.048 0.170 2595 Planarity : 0.005 0.054 3033 Dihedral : 6.457 84.890 2684 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.88 % Allowed : 12.44 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.18), residues: 2121 helix: 2.58 (0.27), residues: 330 sheet: 0.31 (0.21), residues: 555 loop : -0.56 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 435 TYR 0.022 0.003 TYR E 102 PHE 0.040 0.003 PHE C 118 TRP 0.016 0.003 TRP C 343 HIS 0.007 0.002 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00764 (17403) covalent geometry : angle 0.67277 (23604) SS BOND : bond 0.00341 ( 24) SS BOND : angle 1.73762 ( 48) hydrogen bonds : bond 0.05053 ( 696) hydrogen bonds : angle 5.23285 ( 1944) link_BETA1-4 : bond 0.00444 ( 3) link_BETA1-4 : angle 2.23797 ( 9) link_BETA1-6 : bond 0.00335 ( 3) link_BETA1-6 : angle 0.97146 ( 9) link_NAG-ASN : bond 0.00218 ( 12) link_NAG-ASN : angle 1.62372 ( 36) *********************** 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 306 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 234 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 CYS cc_start: 0.7228 (m) cc_final: 0.6896 (m) REVERT: A 88 MET cc_start: 0.8884 (mtp) cc_final: 0.8003 (ttm) REVERT: A 340 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.6815 (pp20) REVERT: A 402 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8111 (mm) REVERT: A 404 ARG cc_start: 0.8307 (mmp-170) cc_final: 0.7951 (mmp-170) REVERT: A 445 LYS cc_start: 0.7832 (mttt) cc_final: 0.7501 (mtmt) REVERT: A 483 ASN cc_start: 0.7615 (t0) cc_final: 0.7241 (m110) REVERT: A 490 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7497 (ttpt) REVERT: B 137 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8178 (mmt90) REVERT: B 195 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7252 (m-80) REVERT: B 278 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7621 (tm-30) REVERT: B 340 GLU cc_start: 0.7876 (mm-30) cc_final: 0.6489 (pp20) REVERT: B 402 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8208 (mm) REVERT: B 445 LYS cc_start: 0.7580 (mttt) cc_final: 0.7169 (mtpt) REVERT: B 479 ASN cc_start: 0.7651 (m110) cc_final: 0.7346 (m-40) REVERT: C 50 LYS cc_start: 0.7354 (mttt) cc_final: 0.6995 (mtpt) REVERT: C 137 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7648 (mpt180) REVERT: C 340 GLU cc_start: 0.8302 (mm-30) cc_final: 0.6531 (pp20) REVERT: C 404 ARG cc_start: 0.8349 (mmp-170) cc_final: 0.8122 (mmp-170) REVERT: C 434 GLU cc_start: 0.8252 (tt0) cc_final: 0.7974 (tt0) REVERT: C 435 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7063 (mtp180) REVERT: C 441 ASP cc_start: 0.8125 (m-30) cc_final: 0.7733 (m-30) REVERT: C 445 LYS cc_start: 0.7590 (mttt) cc_final: 0.7215 (mtpt) REVERT: C 483 ASN cc_start: 0.7409 (t0) cc_final: 0.6918 (m110) REVERT: D 34 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: E 5 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8053 (mm-40) REVERT: E 81 LYS cc_start: 0.8196 (mttp) cc_final: 0.7975 (mttp) REVERT: G 103 LYS cc_start: 0.7895 (ttmm) cc_final: 0.7289 (tptm) REVERT: H 6 GLU cc_start: 0.7815 (mp0) cc_final: 0.7453 (mp0) REVERT: H 34 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: H 70 SER cc_start: 0.8515 (t) cc_final: 0.8095 (m) REVERT: H 105 GLN cc_start: 0.7443 (pm20) cc_final: 0.7047 (pm20) outliers start: 72 outliers final: 47 residues processed: 276 average time/residue: 0.5984 time to fit residues: 185.7591 Evaluate side-chains 281 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 378 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 490 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 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 89 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 25 SER 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 180 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 128 optimal weight: 0.0070 chunk 14 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 298 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 = 0.3562 r_free = 0.3562 target = 0.134825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107298 restraints weight = 19887.790| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.74 r_work: 0.3108 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3532 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= 0.115 Angle : 0.515 7.858 23706 Z= 0.277 Chirality : 0.041 0.221 2595 Planarity : 0.003 0.031 3033 Dihedral : 6.074 86.852 2684 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.42 % Allowed : 14.43 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.18), residues: 2121 helix: 2.90 (0.28), residues: 330 sheet: 0.42 (0.21), residues: 564 loop : -0.44 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 435 TYR 0.014 0.001 TYR E 102 PHE 0.022 0.002 PHE C 118 TRP 0.013 0.001 TRP H 35A HIS 0.005 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00261 (17403) covalent geometry : angle 0.50490 (23604) SS BOND : bond 0.00184 ( 24) SS BOND : angle 1.69358 ( 48) hydrogen bonds : bond 0.04142 ( 696) hydrogen bonds : angle 5.00084 ( 1944) link_BETA1-4 : bond 0.00391 ( 3) link_BETA1-4 : angle 1.79020 ( 9) link_BETA1-6 : bond 0.00554 ( 3) link_BETA1-6 : angle 1.14465 ( 9) link_NAG-ASN : bond 0.00124 ( 12) link_NAG-ASN : angle 1.57583 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8693 (mtp) cc_final: 0.7781 (ttm) REVERT: A 340 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.6817 (pp20) REVERT: A 402 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8134 (mm) REVERT: A 404 ARG cc_start: 0.8268 (mmp-170) cc_final: 0.7967 (mmp-170) REVERT: A 414 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8032 (mp0) REVERT: A 445 LYS cc_start: 0.7638 (mttt) cc_final: 0.7327 (mtmt) REVERT: A 483 ASN cc_start: 0.7716 (t0) cc_final: 0.7377 (m110) REVERT: A 490 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7700 (ttpp) REVERT: B 195 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: B 340 GLU cc_start: 0.7787 (mm-30) cc_final: 0.6421 (pp20) REVERT: B 402 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8253 (mm) REVERT: B 445 LYS cc_start: 0.7534 (mttt) cc_final: 0.7146 (mtpt) REVERT: B 479 ASN cc_start: 0.7683 (m110) cc_final: 0.7402 (m-40) REVERT: C 50 LYS cc_start: 0.7391 (mttt) cc_final: 0.7023 (mtpt) REVERT: C 64 CYS cc_start: 0.7273 (m) cc_final: 0.6901 (m) REVERT: C 137 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7517 (mpt180) REVERT: C 340 GLU cc_start: 0.8252 (mm-30) cc_final: 0.6470 (pp20) REVERT: C 344 GLN cc_start: 0.8676 (mt0) cc_final: 0.8370 (mt0) REVERT: C 432 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8096 (mm-30) REVERT: C 434 GLU cc_start: 0.8191 (tt0) cc_final: 0.7942 (tt0) REVERT: C 435 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7014 (mtp180) REVERT: C 441 ASP cc_start: 0.8021 (m-30) cc_final: 0.7627 (m-30) REVERT: C 445 LYS cc_start: 0.7509 (mttt) cc_final: 0.7114 (mtpt) REVERT: C 483 ASN cc_start: 0.7297 (t0) cc_final: 0.6916 (m110) REVERT: D 34 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: E 5 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8014 (mm-40) REVERT: E 81 LYS cc_start: 0.8135 (mttp) cc_final: 0.7906 (mttp) REVERT: G 103 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7299 (tptm) REVERT: H 6 GLU cc_start: 0.7873 (mp0) cc_final: 0.7428 (mp0) REVERT: H 34 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: H 70 SER cc_start: 0.8413 (t) cc_final: 0.7972 (m) REVERT: H 105 GLN cc_start: 0.7488 (pm20) cc_final: 0.7083 (pm20) REVERT: L 70 THR cc_start: 0.8634 (m) cc_final: 0.8327 (m) outliers start: 45 outliers final: 28 residues processed: 252 average time/residue: 0.5851 time to fit residues: 165.6805 Evaluate side-chains 252 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 490 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 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 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 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 E residue 2 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 25 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 96 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 199 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 298 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 = 0.3550 r_free = 0.3550 target = 0.134087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106449 restraints weight = 19882.151| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.77 r_work: 0.3110 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17445 Z= 0.123 Angle : 0.512 7.361 23706 Z= 0.274 Chirality : 0.041 0.217 2595 Planarity : 0.003 0.030 3033 Dihedral : 5.999 87.875 2684 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.48 % Allowed : 14.65 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 2121 helix: 2.94 (0.28), residues: 330 sheet: 0.53 (0.22), residues: 558 loop : -0.41 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 435 TYR 0.013 0.001 TYR E 102 PHE 0.023 0.002 PHE C 118 TRP 0.016 0.001 TRP B 421 HIS 0.004 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00288 (17403) covalent geometry : angle 0.50269 (23604) SS BOND : bond 0.00189 ( 24) SS BOND : angle 1.56371 ( 48) hydrogen bonds : bond 0.04076 ( 696) hydrogen bonds : angle 4.91122 ( 1944) link_BETA1-4 : bond 0.00377 ( 3) link_BETA1-4 : angle 1.79138 ( 9) link_BETA1-6 : bond 0.00404 ( 3) link_BETA1-6 : angle 1.10031 ( 9) link_NAG-ASN : bond 0.00120 ( 12) link_NAG-ASN : angle 1.57439 ( 36) *********************** 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 271 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8703 (mtp) cc_final: 0.7798 (ttm) REVERT: A 340 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.6829 (pp20) REVERT: A 402 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8168 (mm) REVERT: A 404 ARG cc_start: 0.8277 (mmp-170) cc_final: 0.7984 (mmp-170) REVERT: A 414 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8061 (mp0) REVERT: A 445 LYS cc_start: 0.7621 (mttt) cc_final: 0.7310 (mtmt) REVERT: A 483 ASN cc_start: 0.7563 (t0) cc_final: 0.7296 (m110) REVERT: A 490 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7709 (ttpp) REVERT: B 195 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: B 340 GLU cc_start: 0.7732 (mm-30) cc_final: 0.6322 (pp20) REVERT: B 402 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8176 (mm) REVERT: B 445 LYS cc_start: 0.7512 (mttt) cc_final: 0.7193 (mtpt) REVERT: B 479 ASN cc_start: 0.7593 (m110) cc_final: 0.7314 (m-40) REVERT: C 50 LYS cc_start: 0.7429 (mttt) cc_final: 0.7197 (mtpm) REVERT: C 64 CYS cc_start: 0.7264 (m) cc_final: 0.6902 (m) REVERT: C 137 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7600 (mpt180) REVERT: C 340 GLU cc_start: 0.8222 (mm-30) cc_final: 0.6506 (pp20) REVERT: C 344 GLN cc_start: 0.8684 (mt0) cc_final: 0.8360 (mm-40) REVERT: C 432 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8113 (mm-30) REVERT: C 434 GLU cc_start: 0.8163 (tt0) cc_final: 0.7926 (tt0) REVERT: C 435 ARG cc_start: 0.7813 (mtm110) cc_final: 0.7035 (mtp180) REVERT: C 441 ASP cc_start: 0.8002 (m-30) cc_final: 0.7613 (m-30) REVERT: C 445 LYS cc_start: 0.7471 (mttt) cc_final: 0.7135 (mtmt) REVERT: C 483 ASN cc_start: 0.7280 (t0) cc_final: 0.6897 (m110) REVERT: D 34 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: E 5 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7920 (mm-40) REVERT: E 81 LYS cc_start: 0.8130 (mttp) cc_final: 0.7895 (mttp) REVERT: G 103 LYS cc_start: 0.7807 (ttmm) cc_final: 0.7309 (tptm) REVERT: H 6 GLU cc_start: 0.7847 (mp0) cc_final: 0.7416 (mp0) REVERT: H 34 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: H 105 GLN cc_start: 0.7444 (pm20) cc_final: 0.7030 (pm20) REVERT: L 70 THR cc_start: 0.8616 (m) cc_final: 0.8304 (m) outliers start: 46 outliers final: 33 residues processed: 253 average time/residue: 0.5869 time to fit residues: 167.0619 Evaluate side-chains 263 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 490 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 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 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 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 34 TYR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 159 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 78 optimal weight: 0.0570 chunk 91 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 188 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- 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 196 GLN C 210 ASN ** C 298 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.134378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106545 restraints weight = 19792.877| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.81 r_work: 0.3104 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17445 Z= 0.148 Angle : 0.534 7.414 23706 Z= 0.285 Chirality : 0.042 0.217 2595 Planarity : 0.003 0.031 3033 Dihedral : 6.026 88.303 2684 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.58 % Allowed : 14.86 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.18), residues: 2121 helix: 2.88 (0.28), residues: 330 sheet: 0.51 (0.21), residues: 558 loop : -0.43 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 435 TYR 0.014 0.002 TYR E 102 PHE 0.026 0.002 PHE C 118 TRP 0.013 0.001 TRP H 35A HIS 0.004 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00352 (17403) covalent geometry : angle 0.52417 (23604) SS BOND : bond 0.00215 ( 24) SS BOND : angle 1.77855 ( 48) hydrogen bonds : bond 0.04171 ( 696) hydrogen bonds : angle 4.91674 ( 1944) link_BETA1-4 : bond 0.00380 ( 3) link_BETA1-4 : angle 1.82198 ( 9) link_BETA1-6 : bond 0.00370 ( 3) link_BETA1-6 : angle 1.08077 ( 9) link_NAG-ASN : bond 0.00129 ( 12) link_NAG-ASN : angle 1.58114 ( 36) ********************** 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 271 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8759 (mtp) cc_final: 0.7890 (ttm) REVERT: A 219 THR cc_start: 0.8162 (m) cc_final: 0.7953 (m) REVERT: A 340 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.6830 (pp20) REVERT: A 402 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8144 (mm) REVERT: A 404 ARG cc_start: 0.8259 (mmp-170) cc_final: 0.7964 (mmp-170) REVERT: A 414 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8072 (mp0) REVERT: A 445 LYS cc_start: 0.7625 (mttt) cc_final: 0.7301 (mtmt) REVERT: A 483 ASN cc_start: 0.7581 (t0) cc_final: 0.7291 (m110) REVERT: A 490 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7705 (ttpp) REVERT: B 195 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: B 340 GLU cc_start: 0.7711 (mm-30) cc_final: 0.6364 (pp20) REVERT: B 402 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8177 (mm) REVERT: B 445 LYS cc_start: 0.7466 (mttt) cc_final: 0.7105 (mtpt) REVERT: B 479 ASN cc_start: 0.7587 (m110) cc_final: 0.7303 (m-40) REVERT: C 50 LYS cc_start: 0.7427 (mttt) cc_final: 0.7201 (mtpm) REVERT: C 64 CYS cc_start: 0.7239 (m) cc_final: 0.6876 (m) REVERT: C 137 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7550 (mpt180) REVERT: C 340 GLU cc_start: 0.8253 (mm-30) cc_final: 0.6497 (pp20) REVERT: C 344 GLN cc_start: 0.8691 (mt0) cc_final: 0.8383 (mt0) REVERT: C 432 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8147 (mm-30) REVERT: C 434 GLU cc_start: 0.8193 (tt0) cc_final: 0.7936 (tt0) REVERT: C 435 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7051 (mtp180) REVERT: C 441 ASP cc_start: 0.8033 (m-30) cc_final: 0.7645 (m-30) REVERT: C 445 LYS cc_start: 0.7476 (mttt) cc_final: 0.7184 (mtmt) REVERT: C 483 ASN cc_start: 0.7293 (t0) cc_final: 0.6880 (m110) REVERT: D 34 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: E 5 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8058 (mm-40) REVERT: E 81 LYS cc_start: 0.8123 (mttp) cc_final: 0.7892 (mttp) REVERT: G 103 LYS cc_start: 0.7800 (ttmm) cc_final: 0.7288 (tptm) REVERT: H 2 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7247 (p) REVERT: H 6 GLU cc_start: 0.7839 (mp0) cc_final: 0.7404 (mp0) REVERT: H 34 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: H 70 SER cc_start: 0.8487 (t) cc_final: 0.8060 (m) REVERT: H 105 GLN cc_start: 0.7417 (pm20) cc_final: 0.7011 (pm20) REVERT: L 70 THR cc_start: 0.8611 (m) cc_final: 0.8298 (m) outliers start: 48 outliers final: 33 residues processed: 252 average time/residue: 0.5374 time to fit residues: 152.8324 Evaluate side-chains 260 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 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 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 34 TYR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 38 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 170 optimal weight: 0.0570 chunk 8 optimal weight: 0.0570 chunk 125 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 148 optimal weight: 0.0040 chunk 81 optimal weight: 0.9980 overall best weight: 0.4228 ------------------------------------------------------------------------------- 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 GLN E 5 GLN L 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108969 restraints weight = 19793.327| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.77 r_work: 0.3131 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17445 Z= 0.100 Angle : 0.493 6.537 23706 Z= 0.265 Chirality : 0.041 0.203 2595 Planarity : 0.003 0.030 3033 Dihedral : 5.856 89.757 2684 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.58 % Allowed : 15.13 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.18), residues: 2121 helix: 2.92 (0.28), residues: 333 sheet: 0.54 (0.22), residues: 564 loop : -0.34 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 435 TYR 0.013 0.001 TYR H 53 PHE 0.019 0.001 PHE B 118 TRP 0.016 0.001 TRP B 421 HIS 0.004 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00221 (17403) covalent geometry : angle 0.48433 (23604) SS BOND : bond 0.00206 ( 24) SS BOND : angle 1.58047 ( 48) hydrogen bonds : bond 0.03860 ( 696) hydrogen bonds : angle 4.79007 ( 1944) link_BETA1-4 : bond 0.00332 ( 3) link_BETA1-4 : angle 1.67604 ( 9) link_BETA1-6 : bond 0.00381 ( 3) link_BETA1-6 : angle 1.10742 ( 9) link_NAG-ASN : bond 0.00150 ( 12) link_NAG-ASN : angle 1.48432 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5890.88 seconds wall clock time: 101 minutes 32.33 seconds (6092.33 seconds total)