Starting phenix.real_space_refine on Sun Jun 15 11:31:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tpa_41471/06_2025/8tpa_41471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tpa_41471/06_2025/8tpa_41471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tpa_41471/06_2025/8tpa_41471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tpa_41471/06_2025/8tpa_41471.map" model { file = "/net/cci-nas-00/data/ceres_data/8tpa_41471/06_2025/8tpa_41471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tpa_41471/06_2025/8tpa_41471.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.058 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 69 5.16 5 C 10875 2.51 5 N 2961 2.21 5 O 3381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17286 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1328 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 1, 'TRANS': 161} Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: F, K, C, G, O, N, J, L, I, H Time building chain proxies: 8.50, per 1000 atoms: 0.49 Number of scatterers: 17286 At special positions: 0 Unit cell: (132.25, 127.65, 148.35, 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 69 16.00 O 3381 8.00 N 2961 7.00 C 10875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.06 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.06 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.06 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 132 " " NAG A 402 " - " ASN A 163 " " NAG A 403 " - " ASN A 289 " " NAG A 404 " - " ASN A 63 " " NAG C 401 " - " ASN C 132 " " NAG C 402 " - " ASN C 163 " " NAG C 403 " - " ASN C 289 " " NAG C 404 " - " ASN C 63 " " NAG G 401 " - " ASN G 132 " " NAG G 402 " - " ASN G 163 " " NAG G 403 " - " ASN G 289 " " NAG G 404 " - " ASN G 63 " " NAG M 1 " - " ASN A 95 " " NAG N 1 " - " ASN C 95 " " NAG O 1 " - " ASN G 95 " Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 2.1 seconds 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3960 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 51 sheets defined 21.4% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.773A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU 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 130 removed outlier: 4.213A pdb=" N TRP A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.772A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU 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 130 removed outlier: 4.213A pdb=" N TRP C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 127 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.773A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU G 78 " --> pdb=" O GLU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 112 Processing helix chain 'G' and resid 125 through 130 removed outlier: 4.213A pdb=" N TRP G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 196 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 37 through 58 Processing helix chain 'K' and resid 74 through 127 Processing helix chain 'K' and resid 145 through 155 Processing helix chain 'K' and resid 159 through 161 No H-bonds generated for 'chain 'K' and resid 159 through 161' Processing helix chain 'K' and resid 162 through 171 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.353A pdb=" N ASP 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: 6.121A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.463A 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: 6.632A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.508A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.508A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.368A pdb=" N SER A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N LYS A 144 " --> pdb=" O SER 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 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.858A pdb=" N TYR H 35 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.411A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.411A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 33 through 36 Processing sheet with id=AC1, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.354A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.121A pdb=" N LEU C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.632A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.508A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.508A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.369A pdb=" N SER C 138 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N LYS C 144 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD1, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.858A pdb=" N TYR D 35 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP D 35A" --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR D 50 " --> pdb=" O TRP D 35A" (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.410A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.410A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 33 through 36 Processing sheet with id=AD9, first strand: chain 'G' and resid 24 through 26 removed outlier: 4.353A pdb=" N ASP G 24 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AE2, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'G' and resid 51 through 54 removed outlier: 6.121A pdb=" N LEU G 51 " --> pdb=" O ASP G 275 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS G 277 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.632A pdb=" N LEU G 59 " --> pdb=" O VAL G 88 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 115 through 122 removed outlier: 6.509A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 115 through 122 removed outlier: 6.509A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 136 through 141 removed outlier: 7.368A pdb=" N SER G 138 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N LYS G 144 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AE9, first strand: chain 'G' and resid 286 through 287 Processing sheet with id=AF1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.858A pdb=" N TYR I 35 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP I 35A" --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR I 50 " --> pdb=" O TRP I 35A" (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.409A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA J 84 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.409A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA J 84 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) 777 hydrogen bonds defined for protein. 2070 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: 5.80 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5199 1.33 - 1.47: 5392 1.47 - 1.61: 7013 1.61 - 1.75: 12 1.75 - 1.89: 81 Bond restraints: 17697 Sorted by residual: bond pdb=" CB ILE I 37 " pdb=" CG1 ILE I 37 " ideal model delta sigma weight residual 1.530 1.425 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" CB ILE D 37 " pdb=" CG1 ILE D 37 " ideal model delta sigma weight residual 1.530 1.425 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" CB ILE H 37 " pdb=" CG1 ILE H 37 " ideal model delta sigma weight residual 1.530 1.426 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" CB ASN G 48 " pdb=" CG ASN G 48 " ideal model delta sigma weight residual 1.516 1.391 0.125 2.50e-02 1.60e+03 2.49e+01 bond pdb=" CB ASN C 48 " pdb=" CG ASN C 48 " ideal model delta sigma weight residual 1.516 1.392 0.124 2.50e-02 1.60e+03 2.46e+01 ... (remaining 17692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.57: 23985 7.57 - 15.14: 36 15.14 - 22.71: 0 22.71 - 30.28: 0 30.28 - 37.85: 6 Bond angle restraints: 24027 Sorted by residual: angle pdb=" C2 NAG C 402 " pdb=" N2 NAG C 402 " pdb=" C7 NAG C 402 " ideal model delta sigma weight residual 124.56 162.41 -37.85 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C2 NAG G 402 " pdb=" N2 NAG G 402 " pdb=" C7 NAG G 402 " ideal model delta sigma weight residual 124.56 162.34 -37.78 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C2 NAG A 402 " pdb=" N2 NAG A 402 " pdb=" C7 NAG A 402 " ideal model delta sigma weight residual 124.56 162.31 -37.75 3.00e+00 1.11e-01 1.58e+02 angle pdb=" C2 NAG C 403 " pdb=" N2 NAG C 403 " pdb=" C7 NAG C 403 " ideal model delta sigma weight residual 124.56 160.05 -35.49 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG A 403 " pdb=" N2 NAG A 403 " pdb=" C7 NAG A 403 " ideal model delta sigma weight residual 124.56 160.01 -35.45 3.00e+00 1.11e-01 1.40e+02 ... (remaining 24022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 10314 17.80 - 35.61: 270 35.61 - 53.41: 94 53.41 - 71.22: 35 71.22 - 89.02: 9 Dihedral angle restraints: 10722 sinusoidal: 4503 harmonic: 6219 Sorted by residual: 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 -118.03 32.03 1 1.00e+01 1.00e-02 1.46e+01 dihedral pdb=" CB CYS G 64 " pdb=" SG CYS G 64 " pdb=" SG CYS G 76 " pdb=" CB CYS G 76 " ideal model delta sinusoidal sigma weight residual -86.00 -118.00 32.00 1 1.00e+01 1.00e-02 1.46e+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 -117.98 31.98 1 1.00e+01 1.00e-02 1.46e+01 ... (remaining 10719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1731 0.089 - 0.178: 663 0.178 - 0.267: 150 0.267 - 0.356: 60 0.356 - 0.445: 21 Chirality restraints: 2625 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.03e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.93e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.79e+01 ... (remaining 2622 not shown) Planarity restraints: 3114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 113 " 0.034 2.00e-02 2.50e+03 6.99e-02 4.89e+01 pdb=" C SER D 113 " -0.121 2.00e-02 2.50e+03 pdb=" O SER D 113 " 0.043 2.00e-02 2.50e+03 pdb=" OXT SER D 113 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 113 " 0.034 2.00e-02 2.50e+03 6.96e-02 4.84e+01 pdb=" C SER I 113 " -0.120 2.00e-02 2.50e+03 pdb=" O SER I 113 " 0.043 2.00e-02 2.50e+03 pdb=" OXT SER I 113 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 113 " -0.034 2.00e-02 2.50e+03 6.96e-02 4.84e+01 pdb=" C SER H 113 " 0.120 2.00e-02 2.50e+03 pdb=" O SER H 113 " -0.043 2.00e-02 2.50e+03 pdb=" OXT SER H 113 " -0.043 2.00e-02 2.50e+03 ... (remaining 3111 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 108 2.60 - 3.17: 14366 3.17 - 3.75: 26570 3.75 - 4.32: 39539 4.32 - 4.90: 63985 Nonbonded interactions: 144568 Sorted by model distance: nonbonded pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS I 22 " pdb=" SG CYS I 92 " model vdw 2.024 3.760 ... (remaining 144563 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: 0.22 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.670 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 38.030 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.022 0.152 17727 Z= 1.134 Angle : 1.813 37.848 24105 Z= 1.159 Chirality : 0.106 0.445 2625 Planarity : 0.009 0.070 3099 Dihedral : 10.431 89.023 6726 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2130 helix: 1.50 (0.24), residues: 357 sheet: 0.96 (0.20), residues: 528 loop : 0.54 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.009 TRP C 84 HIS 0.014 0.003 HIS B 142 PHE 0.033 0.006 PHE C 118 TYR 0.086 0.009 TYR I 50 ARG 0.007 0.001 ARG G 192 Details of bonding type rmsd link_NAG-ASN : bond 0.08070 ( 15) link_NAG-ASN : angle 2.78795 ( 45) link_BETA1-4 : bond 0.07326 ( 3) link_BETA1-4 : angle 4.69417 ( 9) hydrogen bonds : bond 0.15410 ( 726) hydrogen bonds : angle 7.61563 ( 2070) SS BOND : bond 0.01812 ( 12) SS BOND : angle 2.80434 ( 24) covalent geometry : bond 0.02168 (17697) covalent geometry : angle 1.80741 (24027) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7298 (mm110) REVERT: B 162 TYR cc_start: 0.7328 (m-80) cc_final: 0.6700 (m-80) REVERT: C 60 GLN cc_start: 0.8554 (mt0) cc_final: 0.8319 (mt0) REVERT: G 274 MET cc_start: 0.7003 (tpt) cc_final: 0.6397 (tpt) outliers start: 0 outliers final: 3 residues processed: 400 average time/residue: 1.4471 time to fit residues: 636.6203 Evaluate side-chains 198 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 195 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain G residue 323 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN L 28 ASN B 26 HIS B 46 ASN B 154 ASN C 33 ASN D 3 GLN D 76 ASN F 26 HIS F 46 ASN G 33 ASN G 73 ASN G 295 GLN I 60 ASN ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 HIS K 46 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120273 restraints weight = 23372.294| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.70 r_work: 0.3218 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17727 Z= 0.180 Angle : 0.717 12.022 24105 Z= 0.370 Chirality : 0.049 0.358 2625 Planarity : 0.005 0.041 3099 Dihedral : 6.379 78.074 2745 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.95 % Allowed : 8.11 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.18), residues: 2130 helix: 2.44 (0.25), residues: 360 sheet: 0.64 (0.20), residues: 579 loop : 0.30 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 47 HIS 0.006 0.001 HIS A 47 PHE 0.036 0.002 PHE A 118 TYR 0.031 0.002 TYR H 50 ARG 0.007 0.001 ARG I 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 15) link_NAG-ASN : angle 2.87188 ( 45) link_BETA1-4 : bond 0.00331 ( 3) link_BETA1-4 : angle 1.87698 ( 9) hydrogen bonds : bond 0.06409 ( 726) hydrogen bonds : angle 6.35994 ( 2070) SS BOND : bond 0.00525 ( 12) SS BOND : angle 2.47866 ( 24) covalent geometry : bond 0.00405 (17697) covalent geometry : angle 0.70246 (24027) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 269 time to evaluate : 1.981 Fit side-chains REVERT: H 16 GLN cc_start: 0.8784 (mt0) cc_final: 0.8531 (mt0) REVERT: B 125 GLN cc_start: 0.7363 (mt0) cc_final: 0.7155 (mt0) REVERT: C 285 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: D 16 GLN cc_start: 0.9002 (mt0) cc_final: 0.8732 (mt0) REVERT: D 63 LEU cc_start: 0.7992 (mt) cc_final: 0.7559 (mt) REVERT: E 24 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7250 (ttt90) REVERT: F 69 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8013 (mm-30) REVERT: G 145 SER cc_start: 0.8759 (m) cc_final: 0.8385 (p) REVERT: G 238 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7826 (mm-30) REVERT: G 274 MET cc_start: 0.7671 (tpt) cc_final: 0.6861 (tpt) REVERT: I 5 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7782 (mmp-170) REVERT: I 16 GLN cc_start: 0.8836 (mt0) cc_final: 0.8537 (mt0) REVERT: I 72 GLU cc_start: 0.7414 (tt0) cc_final: 0.7176 (tt0) REVERT: K 72 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8502 (mttt) REVERT: K 125 GLN cc_start: 0.7573 (mt0) cc_final: 0.7367 (mt0) outliers start: 74 outliers final: 23 residues processed: 313 average time/residue: 1.3120 time to fit residues: 456.7251 Evaluate side-chains 213 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 145 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 170 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN B 26 HIS C 199 ASN D 60 ASN D 76 ASN F 26 HIS F 42 GLN G 199 ASN G 295 GLN ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113203 restraints weight = 23661.872| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.75 r_work: 0.3142 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17727 Z= 0.227 Angle : 0.713 9.505 24105 Z= 0.363 Chirality : 0.050 0.315 2625 Planarity : 0.005 0.033 3099 Dihedral : 6.102 72.903 2739 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.53 % Allowed : 10.72 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2130 helix: 2.10 (0.26), residues: 363 sheet: 0.29 (0.20), residues: 597 loop : -0.16 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 47 HIS 0.009 0.001 HIS C 47 PHE 0.031 0.003 PHE A 118 TYR 0.036 0.002 TYR D 50 ARG 0.008 0.001 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 15) link_NAG-ASN : angle 2.57967 ( 45) link_BETA1-4 : bond 0.00217 ( 3) link_BETA1-4 : angle 1.43226 ( 9) hydrogen bonds : bond 0.05881 ( 726) hydrogen bonds : angle 5.92921 ( 2070) SS BOND : bond 0.00772 ( 12) SS BOND : angle 2.82906 ( 24) covalent geometry : bond 0.00537 (17697) covalent geometry : angle 0.69868 (24027) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 218 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7924 (tp30) REVERT: A 164 LEU cc_start: 0.8308 (mp) cc_final: 0.8061 (mt) REVERT: A 174 LYS cc_start: 0.8724 (mttp) cc_final: 0.8484 (mtpt) REVERT: H 16 GLN cc_start: 0.8858 (mt0) cc_final: 0.8571 (mt0) REVERT: H 43 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.6379 (mmt90) REVERT: C 127 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: C 285 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: C 295 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: D 16 GLN cc_start: 0.8874 (mt0) cc_final: 0.8547 (mt0) REVERT: E 24 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7312 (ttt90) REVERT: E 68 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7229 (mtp85) REVERT: G 145 SER cc_start: 0.8722 (m) cc_final: 0.8481 (p) REVERT: G 238 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7962 (mm-30) REVERT: G 274 MET cc_start: 0.8058 (tpt) cc_final: 0.7160 (tpt) REVERT: I 16 GLN cc_start: 0.8860 (mt0) cc_final: 0.8566 (mt0) REVERT: J 4 MET cc_start: 0.8467 (mmm) cc_final: 0.8140 (mmm) REVERT: J 24 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.6897 (ttt90) REVERT: J 68 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8434 (mtp85) REVERT: K 72 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8541 (mttt) outliers start: 85 outliers final: 39 residues processed: 282 average time/residue: 1.2821 time to fit residues: 402.7698 Evaluate side-chains 242 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 43 ARG Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 145 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 90 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 199 ASN D 3 GLN D 76 ASN F 26 HIS G 33 ASN G 199 ASN I 76 ASN J 31 ASN K 26 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.150506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126029 restraints weight = 23507.884| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.74 r_work: 0.3351 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.003 0.062 17727 Z= 0.148 Angle : 0.615 9.560 24105 Z= 0.311 Chirality : 0.046 0.347 2625 Planarity : 0.004 0.031 3099 Dihedral : 5.773 66.825 2739 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.73 % Allowed : 13.60 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2130 helix: 2.13 (0.26), residues: 363 sheet: 0.20 (0.22), residues: 492 loop : -0.14 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 47 HIS 0.005 0.001 HIS K 26 PHE 0.019 0.002 PHE A 118 TYR 0.029 0.002 TYR H 50 ARG 0.007 0.000 ARG I 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 15) link_NAG-ASN : angle 2.36634 ( 45) link_BETA1-4 : bond 0.00202 ( 3) link_BETA1-4 : angle 1.14943 ( 9) hydrogen bonds : bond 0.05266 ( 726) hydrogen bonds : angle 5.70619 ( 2070) SS BOND : bond 0.00480 ( 12) SS BOND : angle 2.71627 ( 24) covalent geometry : bond 0.00343 (17697) covalent geometry : angle 0.60119 (24027) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 216 time to evaluate : 1.927 Fit side-chains REVERT: A 122 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: A 174 LYS cc_start: 0.8734 (mttp) cc_final: 0.8414 (mtpt) REVERT: H 16 GLN cc_start: 0.8848 (mt0) cc_final: 0.8561 (mt0) REVERT: C 127 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7335 (pt0) REVERT: C 285 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: D 16 GLN cc_start: 0.8899 (mt0) cc_final: 0.8558 (mt0) REVERT: E 68 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7153 (mtp85) REVERT: G 32 LYS cc_start: 0.8257 (ttmm) cc_final: 0.7937 (ttpp) REVERT: G 145 SER cc_start: 0.8718 (m) cc_final: 0.8488 (p) REVERT: G 219 LYS cc_start: 0.8425 (tptt) cc_final: 0.7944 (tptt) REVERT: G 238 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8023 (mm-30) REVERT: G 274 MET cc_start: 0.7873 (tpt) cc_final: 0.6865 (tpt) REVERT: I 16 GLN cc_start: 0.8857 (mt0) cc_final: 0.8536 (mt0) REVERT: I 72 GLU cc_start: 0.7008 (tt0) cc_final: 0.6727 (pp20) REVERT: I 76 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8352 (m-40) REVERT: J 4 MET cc_start: 0.8457 (mmm) cc_final: 0.8148 (mmm) REVERT: J 68 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8481 (mtp85) outliers start: 70 outliers final: 32 residues processed: 267 average time/residue: 1.3075 time to fit residues: 392.1044 Evaluate side-chains 228 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 145 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 56 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 76 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 60 ASN D 76 ASN F 26 HIS G 199 ASN I 76 ASN K 26 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.147781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122690 restraints weight = 23780.157| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.82 r_work: 0.3361 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17727 Z= 0.193 Angle : 0.641 9.636 24105 Z= 0.324 Chirality : 0.047 0.340 2625 Planarity : 0.004 0.031 3099 Dihedral : 5.773 65.469 2739 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.53 % Allowed : 14.19 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2130 helix: 2.08 (0.26), residues: 363 sheet: 0.11 (0.22), residues: 492 loop : -0.23 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 47 HIS 0.005 0.001 HIS K 26 PHE 0.021 0.002 PHE C 118 TYR 0.032 0.002 TYR H 50 ARG 0.007 0.001 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 15) link_NAG-ASN : angle 2.39257 ( 45) link_BETA1-4 : bond 0.00070 ( 3) link_BETA1-4 : angle 1.07733 ( 9) hydrogen bonds : bond 0.05255 ( 726) hydrogen bonds : angle 5.64738 ( 2070) SS BOND : bond 0.00657 ( 12) SS BOND : angle 2.82498 ( 24) covalent geometry : bond 0.00463 (17697) covalent geometry : angle 0.62708 (24027) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 210 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7701 (tp30) REVERT: A 174 LYS cc_start: 0.8623 (mttp) cc_final: 0.8374 (mtpt) REVERT: H 16 GLN cc_start: 0.8898 (mt0) cc_final: 0.8586 (mt0) REVERT: H 37 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7922 (pt) REVERT: C 45 ASP cc_start: 0.8627 (p0) cc_final: 0.8248 (p0) REVERT: C 127 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: C 285 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: C 295 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8559 (pt0) REVERT: D 16 GLN cc_start: 0.8909 (mt0) cc_final: 0.8544 (mt0) REVERT: E 49 TYR cc_start: 0.6376 (OUTLIER) cc_final: 0.6019 (t80) REVERT: E 68 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7203 (mtp85) REVERT: G 32 LYS cc_start: 0.8272 (ttmm) cc_final: 0.7882 (ttpp) REVERT: G 78 LEU cc_start: 0.8813 (mm) cc_final: 0.8586 (tt) REVERT: G 119 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: G 145 SER cc_start: 0.8708 (m) cc_final: 0.8505 (p) REVERT: G 219 LYS cc_start: 0.8419 (tptt) cc_final: 0.7958 (tppp) REVERT: G 238 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8070 (mm-30) REVERT: G 274 MET cc_start: 0.7953 (tpt) cc_final: 0.6900 (tpt) REVERT: I 5 ARG cc_start: 0.7798 (mmp-170) cc_final: 0.7503 (mmp-170) REVERT: I 16 GLN cc_start: 0.8808 (mt0) cc_final: 0.8479 (mt0) REVERT: I 37 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8149 (pt) REVERT: J 4 MET cc_start: 0.8490 (mmm) cc_final: 0.8119 (mmm) REVERT: J 68 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8503 (mtp85) REVERT: K 72 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8508 (mttt) outliers start: 85 outliers final: 38 residues processed: 273 average time/residue: 1.3818 time to fit residues: 421.0111 Evaluate side-chains 251 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 145 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 114 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN B 26 HIS C 33 ASN C 199 ASN D 60 ASN D 76 ASN F 26 HIS I 76 ASN K 26 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125883 restraints weight = 23945.398| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.89 r_work: 0.3329 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17727 Z= 0.179 Angle : 0.628 9.604 24105 Z= 0.317 Chirality : 0.047 0.345 2625 Planarity : 0.004 0.030 3099 Dihedral : 5.752 66.051 2739 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.32 % Allowed : 15.09 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2130 helix: 2.07 (0.26), residues: 363 sheet: 0.09 (0.22), residues: 492 loop : -0.30 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.005 0.001 HIS K 26 PHE 0.019 0.002 PHE C 118 TYR 0.030 0.002 TYR H 50 ARG 0.008 0.001 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 15) link_NAG-ASN : angle 2.31342 ( 45) link_BETA1-4 : bond 0.00179 ( 3) link_BETA1-4 : angle 1.01112 ( 9) hydrogen bonds : bond 0.05109 ( 726) hydrogen bonds : angle 5.62756 ( 2070) SS BOND : bond 0.00599 ( 12) SS BOND : angle 2.96362 ( 24) covalent geometry : bond 0.00428 (17697) covalent geometry : angle 0.61385 (24027) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 212 time to evaluate : 2.309 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: A 173 GLU cc_start: 0.7472 (pt0) cc_final: 0.7114 (tp30) REVERT: A 174 LYS cc_start: 0.8646 (mttp) cc_final: 0.8336 (mtpt) REVERT: H 16 GLN cc_start: 0.8887 (mt0) cc_final: 0.8601 (mt0) REVERT: H 23 THR cc_start: 0.8716 (m) cc_final: 0.8374 (p) REVERT: H 37 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7921 (pt) REVERT: L 22 THR cc_start: 0.8886 (m) cc_final: 0.8616 (m) REVERT: B 39 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6749 (pttt) REVERT: C 45 ASP cc_start: 0.8682 (p0) cc_final: 0.8280 (p0) REVERT: C 127 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: C 285 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: C 295 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8571 (pt0) REVERT: D 16 GLN cc_start: 0.8901 (mt0) cc_final: 0.8523 (mt0) REVERT: D 23 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8149 (p) REVERT: E 49 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.5955 (t80) REVERT: E 68 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7228 (mtp85) REVERT: F 149 MET cc_start: 0.6739 (mmt) cc_final: 0.6531 (mmt) REVERT: G 32 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7935 (ttpp) REVERT: G 78 LEU cc_start: 0.8826 (mm) cc_final: 0.8605 (tt) REVERT: G 119 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: G 145 SER cc_start: 0.8751 (m) cc_final: 0.8544 (p) REVERT: G 219 LYS cc_start: 0.8437 (tptt) cc_final: 0.7984 (tppp) REVERT: G 238 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8175 (mm-30) REVERT: G 274 MET cc_start: 0.7987 (tpt) cc_final: 0.6947 (tpt) REVERT: I 5 ARG cc_start: 0.7888 (mmp-170) cc_final: 0.7467 (mmp-170) REVERT: I 16 GLN cc_start: 0.8811 (mt0) cc_final: 0.8464 (mt0) REVERT: I 37 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8151 (pt) REVERT: I 64 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6519 (ttp80) REVERT: I 76 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8361 (m-40) REVERT: J 4 MET cc_start: 0.8523 (mmm) cc_final: 0.8135 (mmm) REVERT: J 68 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8542 (mtp85) outliers start: 81 outliers final: 43 residues processed: 270 average time/residue: 1.3003 time to fit residues: 392.9090 Evaluate side-chains 253 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 145 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 54 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN B 26 HIS C 33 ASN C 199 ASN D 3 GLN D 76 ASN F 26 HIS F 142 HIS I 76 ASN I 77 GLN J 28 ASN K 26 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.151549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126262 restraints weight = 23896.594| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.89 r_work: 0.3346 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17727 Z= 0.172 Angle : 0.619 9.841 24105 Z= 0.314 Chirality : 0.046 0.341 2625 Planarity : 0.004 0.031 3099 Dihedral : 5.723 66.885 2739 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.32 % Allowed : 15.15 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2130 helix: 2.07 (0.26), residues: 363 sheet: 0.09 (0.23), residues: 492 loop : -0.35 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 35A HIS 0.003 0.001 HIS C 47 PHE 0.018 0.002 PHE C 118 TYR 0.030 0.002 TYR H 50 ARG 0.009 0.000 ARG I 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 15) link_NAG-ASN : angle 2.26642 ( 45) link_BETA1-4 : bond 0.00225 ( 3) link_BETA1-4 : angle 0.97188 ( 9) hydrogen bonds : bond 0.05005 ( 726) hydrogen bonds : angle 5.58371 ( 2070) SS BOND : bond 0.00666 ( 12) SS BOND : angle 2.74975 ( 24) covalent geometry : bond 0.00409 (17697) covalent geometry : angle 0.60522 (24027) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 213 time to evaluate : 2.026 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7721 (tp30) REVERT: A 173 GLU cc_start: 0.7544 (pt0) cc_final: 0.7163 (tp30) REVERT: A 174 LYS cc_start: 0.8615 (mttp) cc_final: 0.8336 (mtpt) REVERT: H 16 GLN cc_start: 0.8888 (mt0) cc_final: 0.8540 (mt0) REVERT: H 23 THR cc_start: 0.8690 (m) cc_final: 0.8361 (p) REVERT: H 37 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7922 (pt) REVERT: L 22 THR cc_start: 0.8858 (m) cc_final: 0.8590 (m) REVERT: B 39 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6664 (pttt) REVERT: C 45 ASP cc_start: 0.8625 (p0) cc_final: 0.8225 (p0) REVERT: C 127 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7389 (pt0) REVERT: D 16 GLN cc_start: 0.8899 (mt0) cc_final: 0.8516 (mt0) REVERT: D 23 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8171 (p) REVERT: E 49 TYR cc_start: 0.6259 (OUTLIER) cc_final: 0.5965 (t80) REVERT: E 68 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7149 (mtp85) REVERT: G 78 LEU cc_start: 0.8801 (mm) cc_final: 0.8592 (tt) REVERT: G 219 LYS cc_start: 0.8351 (tptt) cc_final: 0.7885 (tppp) REVERT: G 238 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8136 (mm-30) REVERT: G 274 MET cc_start: 0.7995 (tpt) cc_final: 0.6889 (tpt) REVERT: I 5 ARG cc_start: 0.7667 (mmp-170) cc_final: 0.7387 (mmp-170) REVERT: I 16 GLN cc_start: 0.8794 (mt0) cc_final: 0.8422 (mt0) REVERT: I 23 THR cc_start: 0.8772 (m) cc_final: 0.8514 (p) REVERT: I 37 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8127 (pt) REVERT: I 64 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6448 (ttp80) REVERT: J 4 MET cc_start: 0.8436 (mmm) cc_final: 0.8167 (mmm) REVERT: K 72 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8514 (mttt) outliers start: 81 outliers final: 48 residues processed: 271 average time/residue: 1.3110 time to fit residues: 398.6725 Evaluate side-chains 252 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 145 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 96 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 ASN H 76 ASN B 26 HIS ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 3 GLN D 54 ASN D 60 ASN D 76 ASN E 79 GLN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.149779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124039 restraints weight = 23854.349| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.93 r_work: 0.3329 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17727 Z= 0.207 Angle : 0.656 11.513 24105 Z= 0.330 Chirality : 0.047 0.374 2625 Planarity : 0.004 0.031 3099 Dihedral : 5.864 67.639 2739 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.75 % Allowed : 15.04 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2130 helix: 2.00 (0.26), residues: 363 sheet: 0.06 (0.23), residues: 492 loop : -0.43 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 35A HIS 0.005 0.001 HIS K 26 PHE 0.022 0.002 PHE C 118 TYR 0.034 0.002 TYR J 49 ARG 0.010 0.001 ARG I 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 15) link_NAG-ASN : angle 2.30289 ( 45) link_BETA1-4 : bond 0.00102 ( 3) link_BETA1-4 : angle 0.91953 ( 9) hydrogen bonds : bond 0.05141 ( 726) hydrogen bonds : angle 5.67086 ( 2070) SS BOND : bond 0.00762 ( 12) SS BOND : angle 3.04552 ( 24) covalent geometry : bond 0.00499 (17697) covalent geometry : angle 0.64240 (24027) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 212 time to evaluate : 1.856 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7926 (tp30) REVERT: A 173 GLU cc_start: 0.7583 (pt0) cc_final: 0.7351 (tp30) REVERT: A 174 LYS cc_start: 0.8657 (mttp) cc_final: 0.8366 (mtpt) REVERT: H 16 GLN cc_start: 0.8889 (mt0) cc_final: 0.8545 (mt0) REVERT: H 23 THR cc_start: 0.8653 (m) cc_final: 0.8334 (p) REVERT: H 37 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7985 (pt) REVERT: L 22 THR cc_start: 0.8899 (m) cc_final: 0.8637 (m) REVERT: B 39 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6667 (pttt) REVERT: B 154 ASN cc_start: 0.6621 (OUTLIER) cc_final: 0.6378 (p0) REVERT: C 45 ASP cc_start: 0.8676 (p0) cc_final: 0.8233 (p0) REVERT: C 127 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7351 (pt0) REVERT: D 5 ARG cc_start: 0.7807 (mmp-170) cc_final: 0.7486 (mmp-170) REVERT: D 16 GLN cc_start: 0.8900 (mt0) cc_final: 0.8525 (mt0) REVERT: D 23 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8312 (p) REVERT: E 49 TYR cc_start: 0.6347 (OUTLIER) cc_final: 0.6048 (t80) REVERT: E 68 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7252 (mtp85) REVERT: G 119 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: G 219 LYS cc_start: 0.8367 (tptt) cc_final: 0.7921 (tppp) REVERT: G 274 MET cc_start: 0.8009 (tpt) cc_final: 0.6895 (tpt) REVERT: I 5 ARG cc_start: 0.7832 (mmp-170) cc_final: 0.7556 (mmp-170) REVERT: I 16 GLN cc_start: 0.8821 (mt0) cc_final: 0.8473 (mt0) REVERT: I 23 THR cc_start: 0.8770 (m) cc_final: 0.8505 (p) REVERT: I 64 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6543 (ttp80) REVERT: I 89 ILE cc_start: 0.8604 (mt) cc_final: 0.8384 (mt) REVERT: J 4 MET cc_start: 0.8442 (mmm) cc_final: 0.8144 (mmm) REVERT: K 72 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8483 (mttt) REVERT: K 98 LEU cc_start: 0.8285 (tp) cc_final: 0.8041 (tp) outliers start: 89 outliers final: 54 residues processed: 278 average time/residue: 1.2839 time to fit residues: 401.3592 Evaluate side-chains 264 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 199 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 145 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 3 optimal weight: 0.0370 chunk 66 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 189 optimal weight: 0.0020 chunk 162 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 overall best weight: 0.9668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 ASN H 76 ASN B 26 HIS C 33 ASN C 133 HIS C 199 ASN D 3 GLN D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.151290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125709 restraints weight = 23860.089| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.92 r_work: 0.3350 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17727 Z= 0.150 Angle : 0.611 11.783 24105 Z= 0.311 Chirality : 0.046 0.326 2625 Planarity : 0.004 0.032 3099 Dihedral : 5.727 68.627 2739 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.95 % Allowed : 15.84 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 2130 helix: 2.08 (0.26), residues: 363 sheet: 0.07 (0.23), residues: 492 loop : -0.41 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 35A HIS 0.005 0.001 HIS K 26 PHE 0.016 0.001 PHE C 118 TYR 0.035 0.002 TYR L 49 ARG 0.010 0.000 ARG I 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 15) link_NAG-ASN : angle 2.15008 ( 45) link_BETA1-4 : bond 0.00256 ( 3) link_BETA1-4 : angle 0.81038 ( 9) hydrogen bonds : bond 0.04815 ( 726) hydrogen bonds : angle 5.56952 ( 2070) SS BOND : bond 0.00458 ( 12) SS BOND : angle 2.79810 ( 24) covalent geometry : bond 0.00357 (17697) covalent geometry : angle 0.59846 (24027) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 205 time to evaluate : 2.060 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: A 173 GLU cc_start: 0.7663 (pt0) cc_final: 0.7187 (tp30) REVERT: A 174 LYS cc_start: 0.8647 (mttp) cc_final: 0.8388 (mtpt) REVERT: H 16 GLN cc_start: 0.8920 (mt0) cc_final: 0.8576 (mt0) REVERT: H 23 THR cc_start: 0.8630 (m) cc_final: 0.8309 (p) REVERT: H 37 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7883 (pt) REVERT: L 4 MET cc_start: 0.8504 (mmm) cc_final: 0.8029 (mmm) REVERT: L 22 THR cc_start: 0.8804 (m) cc_final: 0.8539 (m) REVERT: B 39 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6635 (pttt) REVERT: B 116 LYS cc_start: 0.8148 (mttt) cc_final: 0.7470 (mptt) REVERT: C 45 ASP cc_start: 0.8625 (p0) cc_final: 0.8204 (p0) REVERT: C 127 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: D 5 ARG cc_start: 0.7748 (mmp-170) cc_final: 0.7436 (mmp-170) REVERT: D 16 GLN cc_start: 0.8868 (mt0) cc_final: 0.8469 (mt0) REVERT: D 23 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8296 (p) REVERT: E 68 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7238 (mtp85) REVERT: G 119 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: G 219 LYS cc_start: 0.8371 (tptt) cc_final: 0.7922 (tppp) REVERT: G 238 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8119 (mm-30) REVERT: G 274 MET cc_start: 0.8037 (tpt) cc_final: 0.6941 (tpt) REVERT: I 5 ARG cc_start: 0.7771 (mmp-170) cc_final: 0.7489 (mmp-170) REVERT: I 16 GLN cc_start: 0.8800 (mt0) cc_final: 0.8445 (mt0) REVERT: I 23 THR cc_start: 0.8742 (m) cc_final: 0.8487 (p) REVERT: I 64 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6472 (ttp80) REVERT: J 4 MET cc_start: 0.8367 (mmm) cc_final: 0.8017 (mmm) REVERT: K 98 LEU cc_start: 0.8297 (tp) cc_final: 0.8046 (tp) outliers start: 74 outliers final: 47 residues processed: 260 average time/residue: 1.2485 time to fit residues: 363.2009 Evaluate side-chains 253 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 145 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 110 optimal weight: 0.0000 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS C 199 ASN D 54 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.151243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125637 restraints weight = 23753.552| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.87 r_work: 0.3333 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 17727 Z= 0.216 Angle : 0.987 59.200 24105 Z= 0.590 Chirality : 0.051 0.740 2625 Planarity : 0.005 0.130 3099 Dihedral : 5.744 68.636 2739 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.15 % Allowed : 16.91 % Favored : 79.95 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 2130 helix: 2.09 (0.26), residues: 363 sheet: 0.06 (0.23), residues: 492 loop : -0.41 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 35A HIS 0.004 0.001 HIS K 26 PHE 0.016 0.001 PHE C 118 TYR 0.032 0.002 TYR L 49 ARG 0.008 0.000 ARG I 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 15) link_NAG-ASN : angle 2.14785 ( 45) link_BETA1-4 : bond 0.00238 ( 3) link_BETA1-4 : angle 0.82167 ( 9) hydrogen bonds : bond 0.04851 ( 726) hydrogen bonds : angle 5.56996 ( 2070) SS BOND : bond 0.00501 ( 12) SS BOND : angle 2.71236 ( 24) covalent geometry : bond 0.00454 (17697) covalent geometry : angle 0.98018 (24027) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 1.836 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: A 173 GLU cc_start: 0.7698 (pt0) cc_final: 0.7212 (tp30) REVERT: A 174 LYS cc_start: 0.8671 (mttp) cc_final: 0.8388 (mtpt) REVERT: H 16 GLN cc_start: 0.8912 (mt0) cc_final: 0.8566 (mt0) REVERT: H 23 THR cc_start: 0.8637 (m) cc_final: 0.8310 (p) REVERT: H 37 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7890 (pt) REVERT: L 4 MET cc_start: 0.8583 (mmm) cc_final: 0.8044 (mmm) REVERT: L 22 THR cc_start: 0.8828 (m) cc_final: 0.8568 (m) REVERT: B 39 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6645 (pttt) REVERT: B 116 LYS cc_start: 0.8119 (mttt) cc_final: 0.7422 (mptt) REVERT: B 154 ASN cc_start: 0.6642 (OUTLIER) cc_final: 0.6408 (p0) REVERT: C 45 ASP cc_start: 0.8659 (p0) cc_final: 0.8236 (p0) REVERT: C 127 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7348 (pt0) REVERT: D 5 ARG cc_start: 0.7779 (mmp-170) cc_final: 0.7465 (mmp-170) REVERT: D 16 GLN cc_start: 0.8868 (mt0) cc_final: 0.8466 (mt0) REVERT: D 23 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8306 (p) REVERT: E 68 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7250 (mtp85) REVERT: G 119 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: G 219 LYS cc_start: 0.8384 (tptt) cc_final: 0.7938 (tppp) REVERT: G 238 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8140 (mm-30) REVERT: G 274 MET cc_start: 0.8071 (tpt) cc_final: 0.6974 (tpt) REVERT: I 5 ARG cc_start: 0.7782 (mmp-170) cc_final: 0.7496 (mmp-170) REVERT: I 16 GLN cc_start: 0.8803 (mt0) cc_final: 0.8445 (mt0) REVERT: I 23 THR cc_start: 0.8756 (m) cc_final: 0.8499 (p) REVERT: I 64 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6495 (ttp80) REVERT: J 4 MET cc_start: 0.8386 (mmm) cc_final: 0.8019 (mmm) REVERT: K 98 LEU cc_start: 0.8320 (tp) cc_final: 0.8072 (tp) outliers start: 59 outliers final: 46 residues processed: 244 average time/residue: 1.3483 time to fit residues: 367.4546 Evaluate side-chains 251 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 145 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 69 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS C 199 ASN D 54 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.148323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123702 restraints weight = 23552.611| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.79 r_work: 0.3351 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 17727 Z= 0.216 Angle : 0.987 59.200 24105 Z= 0.590 Chirality : 0.051 0.740 2625 Planarity : 0.005 0.130 3099 Dihedral : 5.744 68.636 2739 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.09 % Allowed : 16.96 % Favored : 79.95 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 2130 helix: 2.09 (0.26), residues: 363 sheet: 0.06 (0.23), residues: 492 loop : -0.41 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 35A HIS 0.004 0.001 HIS K 26 PHE 0.016 0.001 PHE C 118 TYR 0.032 0.002 TYR L 49 ARG 0.008 0.000 ARG I 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 15) link_NAG-ASN : angle 2.14785 ( 45) link_BETA1-4 : bond 0.00238 ( 3) link_BETA1-4 : angle 0.82167 ( 9) hydrogen bonds : bond 0.04851 ( 726) hydrogen bonds : angle 5.56996 ( 2070) SS BOND : bond 0.00501 ( 12) SS BOND : angle 2.71236 ( 24) covalent geometry : bond 0.00454 (17697) covalent geometry : angle 0.98018 (24027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13021.88 seconds wall clock time: 226 minutes 38.69 seconds (13598.69 seconds total)