Starting phenix.real_space_refine on Sun May 18 17:32:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tpa_41471/05_2025/8tpa_41471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tpa_41471/05_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_41471/05_2025/8tpa_41471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tpa_41471/05_2025/8tpa_41471.map" model { file = "/net/cci-nas-00/data/ceres_data/8tpa_41471/05_2025/8tpa_41471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tpa_41471/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.51, 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: 4.39 Conformation dependent library (CDL) restraints added in 2.2 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: 2.84 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: 6.05 Time building geometry restraints manager: 5.10 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: 0.12 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 38.540 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.260 ------------------------------------------------------------------------------- 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 : 2.024 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: 1.4219 time to fit residues: 626.8075 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 : 1.887 ------------------------------------------------------------------------------- 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 = 23372.298| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.70 r_work: 0.3219 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 6.35995 ( 2070) SS BOND : bond 0.00525 ( 12) SS BOND : angle 2.47865 ( 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 : 1.879 Fit side-chains REVERT: H 16 GLN cc_start: 0.8785 (mt0) cc_final: 0.8532 (mt0) REVERT: B 125 GLN cc_start: 0.7365 (mt0) cc_final: 0.7159 (mt0) REVERT: C 285 GLN cc_start: 0.8347 (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: 0.7990 (mt) cc_final: 0.7559 (mt) REVERT: E 24 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7253 (ttt90) REVERT: F 69 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8012 (mm-30) REVERT: G 145 SER cc_start: 0.8758 (m) cc_final: 0.8385 (p) REVERT: G 238 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7826 (mm-30) REVERT: G 274 MET cc_start: 0.7670 (tpt) cc_final: 0.6860 (tpt) REVERT: I 5 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7781 (mmp-170) REVERT: I 16 GLN cc_start: 0.8836 (mt0) cc_final: 0.8538 (mt0) REVERT: I 72 GLU cc_start: 0.7413 (tt0) cc_final: 0.7175 (tt0) REVERT: K 72 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8501 (mttt) REVERT: K 125 GLN cc_start: 0.7577 (mt0) cc_final: 0.7372 (mt0) outliers start: 74 outliers final: 23 residues processed: 313 average time/residue: 1.2451 time to fit residues: 434.8014 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 : 2.054 ------------------------------------------------------------------------------- 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: 0.1980 chunk 162 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 K 26 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115859 restraints weight = 23568.656| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.70 r_work: 0.3181 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17727 Z= 0.193 Angle : 0.669 9.491 24105 Z= 0.341 Chirality : 0.048 0.294 2625 Planarity : 0.004 0.034 3099 Dihedral : 5.980 74.575 2739 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.48 % Allowed : 10.51 % Favored : 85.01 % 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: 0.61 (0.17), residues: 2130 helix: 2.20 (0.25), residues: 363 sheet: 0.33 (0.20), residues: 597 loop : -0.06 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 47 HIS 0.008 0.001 HIS C 47 PHE 0.028 0.002 PHE C 118 TYR 0.032 0.002 TYR H 50 ARG 0.008 0.001 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 15) link_NAG-ASN : angle 2.52708 ( 45) link_BETA1-4 : bond 0.00224 ( 3) link_BETA1-4 : angle 1.34017 ( 9) hydrogen bonds : bond 0.05742 ( 726) hydrogen bonds : angle 5.91112 ( 2070) SS BOND : bond 0.00675 ( 12) SS BOND : angle 2.94888 ( 24) covalent geometry : bond 0.00452 (17697) covalent geometry : angle 0.65436 (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: 84 poor density : 219 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7861 (tp30) REVERT: A 164 LEU cc_start: 0.8232 (mp) cc_final: 0.7979 (mt) REVERT: A 274 MET cc_start: 0.8324 (tpt) cc_final: 0.8074 (tpt) REVERT: A 295 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8606 (pt0) REVERT: H 5 ARG cc_start: 0.8068 (mmp-170) cc_final: 0.7852 (mmp-170) REVERT: H 16 GLN cc_start: 0.8836 (mt0) cc_final: 0.8538 (mt0) REVERT: C 127 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7391 (pt0) REVERT: C 174 LYS cc_start: 0.8802 (mttp) cc_final: 0.8564 (mttt) REVERT: C 285 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: C 295 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: D 16 GLN cc_start: 0.8919 (mt0) cc_final: 0.8583 (mt0) REVERT: E 24 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7306 (ttt90) REVERT: E 68 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7166 (mtp85) REVERT: G 145 SER cc_start: 0.8683 (m) cc_final: 0.8396 (p) REVERT: G 219 LYS cc_start: 0.8484 (tptt) cc_final: 0.8051 (tptt) REVERT: G 238 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7875 (mm-30) REVERT: G 274 MET cc_start: 0.7890 (tpt) cc_final: 0.6954 (tpt) REVERT: I 16 GLN cc_start: 0.8850 (mt0) cc_final: 0.8556 (mt0) REVERT: I 57 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8575 (p) REVERT: J 4 MET cc_start: 0.8429 (mmm) cc_final: 0.8096 (mmm) REVERT: J 68 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8306 (mtp85) REVERT: K 72 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8520 (mttt) outliers start: 84 outliers final: 39 residues processed: 281 average time/residue: 1.2258 time to fit residues: 384.4139 Evaluate side-chains 240 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 57 THR 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 B residue 152 VAL Chi-restraints excluded: chain C residue 27 ASP 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 58 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 144 CYS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 80 ILE 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 50 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 72 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 90 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 176 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 115 optimal weight: 0.0050 chunk 131 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN H 76 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 199 ASN D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3869 r_free = 0.3869 target = 0.152097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127492 restraints weight = 23532.539| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.82 r_work: 0.3444 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17727 Z= 0.129 Angle : 0.592 9.558 24105 Z= 0.301 Chirality : 0.046 0.326 2625 Planarity : 0.004 0.029 3099 Dihedral : 5.653 66.937 2739 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.25 % Allowed : 13.60 % Favored : 83.15 % 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: 0.63 (0.17), residues: 2130 helix: 2.29 (0.25), residues: 363 sheet: 0.29 (0.23), residues: 474 loop : -0.02 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.008 0.001 HIS B 142 PHE 0.018 0.001 PHE C 118 TYR 0.026 0.002 TYR D 50 ARG 0.007 0.000 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 15) link_NAG-ASN : angle 2.28433 ( 45) link_BETA1-4 : bond 0.00191 ( 3) link_BETA1-4 : angle 1.14220 ( 9) hydrogen bonds : bond 0.05130 ( 726) hydrogen bonds : angle 5.66800 ( 2070) SS BOND : bond 0.00580 ( 12) SS BOND : angle 2.76119 ( 24) covalent geometry : bond 0.00287 (17697) covalent geometry : angle 0.57819 (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 271 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 210 time to evaluate : 1.777 Fit side-chains REVERT: H 16 GLN cc_start: 0.8925 (mt0) cc_final: 0.8615 (mt0) REVERT: C 127 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7325 (pt0) REVERT: C 174 LYS cc_start: 0.8830 (mttp) cc_final: 0.8617 (mttt) REVERT: C 285 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: D 16 GLN cc_start: 0.8985 (mt0) cc_final: 0.8621 (mt0) REVERT: E 68 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.6984 (mtp85) REVERT: G 32 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7938 (ttpp) REVERT: G 145 SER cc_start: 0.8649 (m) cc_final: 0.8378 (p) REVERT: G 219 LYS cc_start: 0.8356 (tptt) cc_final: 0.7875 (tptt) REVERT: G 238 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7914 (mm-30) REVERT: G 274 MET cc_start: 0.7687 (tpt) cc_final: 0.6852 (tpt) REVERT: I 16 GLN cc_start: 0.8873 (mt0) cc_final: 0.8559 (mt0) REVERT: I 72 GLU cc_start: 0.6944 (tt0) cc_final: 0.6712 (pp20) REVERT: J 4 MET cc_start: 0.8402 (mmm) cc_final: 0.8092 (mmm) outliers start: 61 outliers final: 28 residues processed: 257 average time/residue: 1.2881 time to fit residues: 369.3211 Evaluate side-chains 215 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 51 ILE 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 B residue 121 LYS Chi-restraints excluded: chain B residue 145 ASN 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 D residue 18 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 58 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 145 ASN Chi-restraints excluded: chain I residue 7 SER 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 K residue 144 CYS 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: 0.3980 chunk 90 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 60 ASN D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3860 r_free = 0.3860 target = 0.152237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.126781 restraints weight = 24103.999| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.89 r_work: 0.3315 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17727 Z= 0.191 Angle : 0.633 9.620 24105 Z= 0.320 Chirality : 0.047 0.339 2625 Planarity : 0.004 0.029 3099 Dihedral : 5.706 65.536 2739 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.79 % Allowed : 14.40 % Favored : 81.81 % 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: 0.43 (0.17), residues: 2130 helix: 2.18 (0.25), residues: 363 sheet: 0.17 (0.22), residues: 492 loop : -0.18 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35A HIS 0.005 0.001 HIS C 47 PHE 0.023 0.002 PHE C 118 TYR 0.032 0.002 TYR I 50 ARG 0.007 0.001 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 15) link_NAG-ASN : angle 2.36078 ( 45) link_BETA1-4 : bond 0.00178 ( 3) link_BETA1-4 : angle 1.13044 ( 9) hydrogen bonds : bond 0.05239 ( 726) hydrogen bonds : angle 5.63185 ( 2070) SS BOND : bond 0.00793 ( 12) SS BOND : angle 2.89515 ( 24) covalent geometry : bond 0.00453 (17697) covalent geometry : angle 0.61835 (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 281 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 210 time to evaluate : 1.871 Fit side-chains revert: symmetry clash REVERT: H 16 GLN cc_start: 0.8925 (mt0) cc_final: 0.8595 (mt0) REVERT: H 43 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6600 (mmm-85) REVERT: C 127 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7389 (pt0) REVERT: C 285 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: C 295 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8532 (pt0) REVERT: D 16 GLN cc_start: 0.8912 (mt0) cc_final: 0.8547 (mt0) REVERT: E 68 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7176 (mtp85) REVERT: G 32 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7978 (ttpp) REVERT: G 78 LEU cc_start: 0.8789 (mm) cc_final: 0.8529 (tt) REVERT: G 145 SER cc_start: 0.8726 (m) cc_final: 0.8492 (p) REVERT: G 219 LYS cc_start: 0.8454 (tptt) cc_final: 0.7973 (tptt) REVERT: G 238 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8030 (mm-30) REVERT: G 274 MET cc_start: 0.7974 (tpt) cc_final: 0.6964 (tpt) REVERT: I 16 GLN cc_start: 0.8868 (mt0) cc_final: 0.8522 (mt0) REVERT: I 37 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7906 (pt) outliers start: 71 outliers final: 36 residues processed: 263 average time/residue: 1.2159 time to fit residues: 357.0357 Evaluate side-chains 236 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 76 ASN Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 114 optimal weight: 0.1980 chunk 115 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 44 optimal weight: 0.0570 chunk 189 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.4502 ------------------------------------------------------------------------------- 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 18 HIS C 33 ASN C 199 ASN D 60 ASN D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN I 76 ASN K 26 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124994 restraints weight = 23811.812| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.06 r_work: 0.3361 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17727 Z= 0.189 Angle : 0.631 9.617 24105 Z= 0.318 Chirality : 0.047 0.330 2625 Planarity : 0.004 0.030 3099 Dihedral : 5.735 65.809 2739 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.05 % Allowed : 14.93 % Favored : 81.01 % 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: 0.36 (0.17), residues: 2130 helix: 2.14 (0.26), residues: 363 sheet: 0.16 (0.22), residues: 492 loop : -0.25 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 103 HIS 0.005 0.001 HIS K 26 PHE 0.021 0.002 PHE C 118 TYR 0.031 0.002 TYR L 49 ARG 0.008 0.001 ARG I 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 15) link_NAG-ASN : angle 2.31870 ( 45) link_BETA1-4 : bond 0.00044 ( 3) link_BETA1-4 : angle 1.04545 ( 9) hydrogen bonds : bond 0.05151 ( 726) hydrogen bonds : angle 5.63987 ( 2070) SS BOND : bond 0.00722 ( 12) SS BOND : angle 2.99983 ( 24) covalent geometry : bond 0.00451 (17697) covalent geometry : angle 0.61599 (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 280 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 204 time to evaluate : 2.069 Fit side-chains revert: symmetry clash REVERT: H 16 GLN cc_start: 0.8850 (mt0) cc_final: 0.8538 (mt0) REVERT: H 23 THR cc_start: 0.8687 (m) cc_final: 0.8346 (p) REVERT: H 37 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7962 (pt) REVERT: C 127 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: C 285 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: C 295 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8556 (pt0) REVERT: D 16 GLN cc_start: 0.8898 (mt0) cc_final: 0.8512 (mt0) REVERT: E 49 TYR cc_start: 0.6262 (OUTLIER) cc_final: 0.5923 (t80) REVERT: E 68 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7178 (mtp85) REVERT: G 32 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7886 (ttpp) REVERT: G 78 LEU cc_start: 0.8780 (mm) cc_final: 0.8571 (tt) REVERT: G 145 SER cc_start: 0.8722 (m) cc_final: 0.8509 (p) REVERT: G 219 LYS cc_start: 0.8396 (tptt) cc_final: 0.7940 (tppp) REVERT: G 238 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8059 (mm-30) REVERT: G 274 MET cc_start: 0.7946 (tpt) cc_final: 0.6922 (tpt) REVERT: I 16 GLN cc_start: 0.8807 (mt0) cc_final: 0.8444 (mt0) REVERT: I 37 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.8022 (pt) REVERT: J 4 MET cc_start: 0.8443 (mmm) cc_final: 0.8099 (mmm) REVERT: K 72 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8498 (mttt) outliers start: 76 outliers final: 39 residues processed: 260 average time/residue: 1.2097 time to fit residues: 353.0283 Evaluate side-chains 240 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 2.090 ------------------------------------------------------------------------------- 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 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 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 53 THR Chi-restraints excluded: chain B residue 55 VAL 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 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 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 145 ASN 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 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 K residue 72 LYS Chi-restraints excluded: chain K residue 126 LEU 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: 0.7980 chunk 38 optimal weight: 0.2980 chunk 148 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 F 142 HIS G 199 ASN I 76 ASN K 26 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.152266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.126753 restraints weight = 23762.470| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.90 r_work: 0.3339 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17727 Z= 0.151 Angle : 0.597 10.213 24105 Z= 0.303 Chirality : 0.046 0.329 2625 Planarity : 0.004 0.031 3099 Dihedral : 5.645 66.981 2739 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.79 % Allowed : 15.15 % Favored : 81.07 % 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: 0.33 (0.18), residues: 2130 helix: 2.15 (0.26), residues: 363 sheet: 0.15 (0.23), residues: 492 loop : -0.28 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 35A HIS 0.004 0.001 HIS G 47 PHE 0.017 0.002 PHE C 118 TYR 0.028 0.002 TYR I 50 ARG 0.008 0.000 ARG H 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 15) link_NAG-ASN : angle 2.17838 ( 45) link_BETA1-4 : bond 0.00238 ( 3) link_BETA1-4 : angle 0.95132 ( 9) hydrogen bonds : bond 0.04894 ( 726) hydrogen bonds : angle 5.55166 ( 2070) SS BOND : bond 0.00546 ( 12) SS BOND : angle 2.70608 ( 24) covalent geometry : bond 0.00355 (17697) covalent geometry : angle 0.58387 (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 284 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 213 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.8861 (mt0) cc_final: 0.8526 (mt0) REVERT: H 23 THR cc_start: 0.8707 (m) cc_final: 0.8369 (p) REVERT: H 37 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7857 (pt) REVERT: B 39 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6632 (pttt) REVERT: B 57 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: C 127 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: C 285 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: D 16 GLN cc_start: 0.8916 (mt0) cc_final: 0.8528 (mt0) REVERT: E 68 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7185 (mtp85) REVERT: G 78 LEU cc_start: 0.8792 (mm) cc_final: 0.8576 (tt) REVERT: G 119 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: G 145 SER cc_start: 0.8731 (m) cc_final: 0.8524 (p) REVERT: G 219 LYS cc_start: 0.8373 (tptt) cc_final: 0.7905 (tppp) REVERT: G 238 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8151 (mm-30) REVERT: G 274 MET cc_start: 0.7957 (tpt) cc_final: 0.6946 (tpt) REVERT: I 16 GLN cc_start: 0.8789 (mt0) cc_final: 0.8415 (mt0) REVERT: I 23 THR cc_start: 0.8671 (m) cc_final: 0.8439 (p) REVERT: I 37 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8015 (pt) REVERT: I 76 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8227 (m-40) REVERT: J 4 MET cc_start: 0.8440 (mmm) cc_final: 0.8073 (mmm) outliers start: 71 outliers final: 39 residues processed: 262 average time/residue: 1.1821 time to fit residues: 348.4234 Evaluate side-chains 245 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 1.876 ------------------------------------------------------------------------------- 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 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 B residue 39 LYS Chi-restraints excluded: chain B residue 55 VAL 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 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 D residue 21 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 38 ARG 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 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 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 37 ILE 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 K residue 144 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 96 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 187 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 60 ASN D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN I 77 GLN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.151965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126411 restraints weight = 23701.937| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.92 r_work: 0.3323 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17727 Z= 0.158 Angle : 0.609 11.081 24105 Z= 0.309 Chirality : 0.046 0.315 2625 Planarity : 0.004 0.032 3099 Dihedral : 5.649 67.777 2739 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.79 % Allowed : 15.31 % Favored : 80.91 % 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: 0.31 (0.18), residues: 2130 helix: 2.15 (0.26), residues: 363 sheet: 0.16 (0.23), residues: 492 loop : -0.31 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 35A HIS 0.005 0.001 HIS K 26 PHE 0.018 0.002 PHE C 118 TYR 0.032 0.002 TYR I 50 ARG 0.009 0.000 ARG I 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 15) link_NAG-ASN : angle 2.16780 ( 45) link_BETA1-4 : bond 0.00211 ( 3) link_BETA1-4 : angle 0.89667 ( 9) hydrogen bonds : bond 0.04848 ( 726) hydrogen bonds : angle 5.54145 ( 2070) SS BOND : bond 0.00544 ( 12) SS BOND : angle 3.01605 ( 24) covalent geometry : bond 0.00377 (17697) covalent geometry : angle 0.59483 (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 278 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 207 time to evaluate : 1.827 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7582 (pt0) cc_final: 0.7266 (tp30) REVERT: H 16 GLN cc_start: 0.8889 (mt0) cc_final: 0.8548 (mt0) REVERT: H 23 THR cc_start: 0.8692 (m) cc_final: 0.8366 (p) REVERT: H 37 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7938 (pt) REVERT: L 4 MET cc_start: 0.8459 (mmm) cc_final: 0.7977 (mmm) REVERT: B 57 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: C 127 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7411 (pt0) REVERT: D 5 ARG cc_start: 0.7945 (mmp-170) cc_final: 0.7641 (mmp-170) REVERT: D 16 GLN cc_start: 0.8915 (mt0) cc_final: 0.8526 (mt0) REVERT: D 23 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8198 (p) REVERT: E 68 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7191 (mtp85) REVERT: G 119 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: G 145 SER cc_start: 0.8766 (m) cc_final: 0.8560 (p) REVERT: G 219 LYS cc_start: 0.8347 (tptt) cc_final: 0.7894 (tppp) REVERT: G 238 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8154 (mm-30) REVERT: G 274 MET cc_start: 0.7962 (tpt) cc_final: 0.6890 (tpt) REVERT: I 16 GLN cc_start: 0.8776 (mt0) cc_final: 0.8406 (mt0) REVERT: I 23 THR cc_start: 0.8746 (m) cc_final: 0.8469 (p) REVERT: I 37 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8080 (pt) REVERT: J 4 MET cc_start: 0.8442 (mmm) cc_final: 0.8061 (mmm) REVERT: K 72 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8509 (mttt) outliers start: 71 outliers final: 41 residues processed: 259 average time/residue: 1.1908 time to fit residues: 347.1395 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 : 1.805 ------------------------------------------------------------------------------- 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 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 B residue 55 VAL 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 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 38 ARG 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 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 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 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 144 CYS Chi-restraints excluded: chain K residue 148 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 3 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 199 ASN D 54 ASN D 76 ASN D 77 GLN E 79 GLN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN 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 = 0.3827 r_free = 0.3827 target = 0.148655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122989 restraints weight = 23955.491| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.92 r_work: 0.3311 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 17727 Z= 0.257 Angle : 0.705 11.927 24105 Z= 0.355 Chirality : 0.049 0.410 2625 Planarity : 0.005 0.038 3099 Dihedral : 6.058 68.108 2739 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.57 % Allowed : 15.95 % Favored : 80.48 % 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: 0.15 (0.17), residues: 2130 helix: 2.02 (0.26), residues: 360 sheet: 0.32 (0.23), residues: 462 loop : -0.52 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 35A HIS 0.007 0.001 HIS C 47 PHE 0.024 0.002 PHE C 118 TYR 0.045 0.002 TYR E 49 ARG 0.011 0.001 ARG I 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 15) link_NAG-ASN : angle 2.36339 ( 45) link_BETA1-4 : bond 0.00055 ( 3) link_BETA1-4 : angle 0.96055 ( 9) hydrogen bonds : bond 0.05361 ( 726) hydrogen bonds : angle 5.76209 ( 2070) SS BOND : bond 0.00902 ( 12) SS BOND : angle 3.01443 ( 24) covalent geometry : bond 0.00623 (17697) covalent geometry : angle 0.69230 (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 286 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 219 time to evaluate : 1.805 Fit side-chains revert: symmetry clash REVERT: H 16 GLN cc_start: 0.8901 (mt0) cc_final: 0.8543 (mt0) REVERT: H 23 THR cc_start: 0.8748 (m) cc_final: 0.8425 (p) REVERT: H 37 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8103 (pt) REVERT: L 4 MET cc_start: 0.8485 (mmm) cc_final: 0.7937 (mmm) REVERT: L 22 THR cc_start: 0.8908 (m) cc_final: 0.8643 (m) REVERT: B 57 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: B 154 ASN cc_start: 0.6585 (OUTLIER) cc_final: 0.6378 (p0) REVERT: C 127 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7404 (pt0) REVERT: D 5 ARG cc_start: 0.7972 (mmp-170) cc_final: 0.7656 (mmp-170) REVERT: D 16 GLN cc_start: 0.8871 (mt0) cc_final: 0.8471 (mt0) REVERT: D 23 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8275 (p) REVERT: E 68 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7244 (mtp85) REVERT: G 119 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: G 219 LYS cc_start: 0.8468 (tptt) cc_final: 0.8035 (tppp) REVERT: G 274 MET cc_start: 0.8129 (tpt) cc_final: 0.7057 (tpt) REVERT: I 16 GLN cc_start: 0.8815 (mt0) cc_final: 0.8450 (mt0) REVERT: I 64 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6637 (ttp80) REVERT: I 76 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8388 (m-40) REVERT: I 89 ILE cc_start: 0.8622 (mt) cc_final: 0.8400 (mt) REVERT: J 4 MET cc_start: 0.8421 (mmm) cc_final: 0.8035 (mmm) REVERT: K 72 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8528 (mttt) outliers start: 67 outliers final: 44 residues processed: 270 average time/residue: 1.1695 time to fit residues: 354.9205 Evaluate side-chains 255 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 201 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 304 GLU 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 53 THR Chi-restraints excluded: chain B residue 55 VAL 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 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 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 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 33 LEU Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 144 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 110 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 199 ASN D 3 GLN D 54 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN D 77 GLN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN ** J 28 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.148811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122921 restraints weight = 23830.431| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.98 r_work: 0.3308 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 17727 Z= 0.259 Angle : 0.976 59.200 24105 Z= 0.558 Chirality : 0.050 0.565 2625 Planarity : 0.005 0.038 3099 Dihedral : 6.064 68.139 2739 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.09 % Allowed : 16.69 % Favored : 80.21 % Cbeta Deviations : 0.10 % 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: 2.03 (0.26), residues: 360 sheet: 0.30 (0.23), residues: 462 loop : -0.53 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 103 HIS 0.005 0.001 HIS C 47 PHE 0.023 0.002 PHE C 118 TYR 0.041 0.002 TYR E 49 ARG 0.010 0.001 ARG I 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 15) link_NAG-ASN : angle 2.36661 ( 45) link_BETA1-4 : bond 0.00570 ( 3) link_BETA1-4 : angle 1.14289 ( 9) hydrogen bonds : bond 0.05278 ( 726) hydrogen bonds : angle 5.76307 ( 2070) SS BOND : bond 0.00995 ( 12) SS BOND : angle 3.05967 ( 24) covalent geometry : bond 0.00587 (17697) covalent geometry : angle 0.96715 (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 260 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 1.799 Fit side-chains revert: symmetry clash REVERT: H 16 GLN cc_start: 0.8894 (mt0) cc_final: 0.8533 (mt0) REVERT: H 23 THR cc_start: 0.8753 (m) cc_final: 0.8423 (p) REVERT: H 37 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8095 (pt) REVERT: L 22 THR cc_start: 0.8910 (m) cc_final: 0.8650 (m) REVERT: B 57 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: B 154 ASN cc_start: 0.6584 (OUTLIER) cc_final: 0.6378 (p0) REVERT: C 127 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7425 (pt0) REVERT: D 5 ARG cc_start: 0.7973 (mmp-170) cc_final: 0.7657 (mmp-170) REVERT: D 16 GLN cc_start: 0.8871 (mt0) cc_final: 0.8464 (mt0) REVERT: D 23 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8289 (p) REVERT: E 68 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7247 (mtp85) REVERT: G 119 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: G 219 LYS cc_start: 0.8477 (tptt) cc_final: 0.8041 (tppp) REVERT: G 274 MET cc_start: 0.8149 (tpt) cc_final: 0.7093 (tpt) REVERT: I 16 GLN cc_start: 0.8810 (mt0) cc_final: 0.8440 (mt0) REVERT: I 64 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6639 (ttp80) REVERT: I 89 ILE cc_start: 0.8626 (mt) cc_final: 0.8404 (mt) REVERT: J 4 MET cc_start: 0.8425 (mmm) cc_final: 0.8027 (mmm) REVERT: K 72 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8533 (mttt) outliers start: 58 outliers final: 44 residues processed: 246 average time/residue: 1.1818 time to fit residues: 326.6262 Evaluate side-chains 253 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 1.796 ------------------------------------------------------------------------------- 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 304 GLU 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 L residue 53 THR Chi-restraints excluded: chain B residue 55 VAL 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 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 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 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 144 CYS 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: 2.9990 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 3 GLN D 54 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN D 77 GLN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN ** J 28 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.148807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123191 restraints weight = 23830.600| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.88 r_work: 0.3313 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 17727 Z= 0.259 Angle : 0.976 59.200 24105 Z= 0.558 Chirality : 0.050 0.565 2625 Planarity : 0.005 0.038 3099 Dihedral : 6.064 68.139 2739 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.04 % Allowed : 16.75 % Favored : 80.21 % Cbeta Deviations : 0.10 % 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: 2.03 (0.26), residues: 360 sheet: 0.30 (0.23), residues: 462 loop : -0.53 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 103 HIS 0.005 0.001 HIS C 47 PHE 0.023 0.002 PHE C 118 TYR 0.041 0.002 TYR E 49 ARG 0.010 0.001 ARG I 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 15) link_NAG-ASN : angle 2.36661 ( 45) link_BETA1-4 : bond 0.00570 ( 3) link_BETA1-4 : angle 1.14289 ( 9) hydrogen bonds : bond 0.05278 ( 726) hydrogen bonds : angle 5.76307 ( 2070) SS BOND : bond 0.01709 ( 12) SS BOND : angle 3.11826 ( 24) covalent geometry : bond 0.00587 (17697) covalent geometry : angle 0.96715 (24027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11757.07 seconds wall clock time: 203 minutes 30.23 seconds (12210.23 seconds total)