Starting phenix.real_space_refine on Sat Jul 4 00:50:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tpa_41471/07_2026/8tpa_41471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tpa_41471/07_2026/8tpa_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8tpa_41471/07_2026/8tpa_41471.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tpa_41471/07_2026/8tpa_41471.cif" model { file = "/net/cci-nas-00/data/ceres_data/8tpa_41471/07_2026/8tpa_41471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tpa_41471/07_2026/8tpa_41471.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tpa_41471/07_2026/8tpa_41471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tpa_41471/07_2026/8tpa_41471.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.058 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: "H" 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: "L" 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: "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: "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 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 chiralities: 4 Restraints were copied for chains: C, G, D, I, E, J, F, K, N, O Time building chain proxies: 3.75, per 1000 atoms: 0.22 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=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.05 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 H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS F 137 " distance=2.05 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS K 137 " distance=2.05 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS K 144 " - pdb=" SG CYS K 148 " distance=2.03 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: 1.69 Conformation dependent library (CDL) restraints added in 728.8 milliseconds 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: 0.69 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: 3.63 Time building geometry restraints manager: 2.19 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: 9975 17.80 - 35.61: 261 35.61 - 53.41: 97 53.41 - 71.22: 38 71.22 - 89.02: 9 Dihedral angle restraints: 10380 sinusoidal: 4161 harmonic: 6219 Sorted by residual: dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual 93.00 146.69 -53.69 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CB CYS K 144 " pdb=" SG CYS K 144 " pdb=" SG CYS K 148 " pdb=" CB CYS K 148 " ideal model delta sinusoidal sigma weight residual 93.00 146.67 -53.67 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual 93.00 146.66 -53.66 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 10377 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: 2.34 - 2.85: 5534 2.85 - 3.36: 15252 3.36 - 3.88: 30199 3.88 - 4.39: 35145 4.39 - 4.90: 58402 Nonbonded interactions: 144532 Sorted by model distance: nonbonded pdb=" NZ LYS B 83 " pdb=" OD1 ASP F 85 " model vdw 2.338 3.120 nonbonded pdb=" OD1 ASP B 85 " pdb=" NZ LYS K 83 " model vdw 2.338 3.120 nonbonded pdb=" NZ LYS F 83 " pdb=" OD1 ASP K 85 " model vdw 2.338 3.120 nonbonded pdb=" N ALA J 50 " pdb=" O ALA J 50 " model vdw 2.355 2.496 nonbonded pdb=" N ALA L 50 " pdb=" O ALA L 50 " model vdw 2.355 2.496 ... (remaining 144527 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 17739 Z= 1.133 Angle : 1.816 37.848 24129 Z= 1.160 Chirality : 0.106 0.445 2625 Planarity : 0.009 0.070 3099 Dihedral : 10.433 89.023 6348 Min Nonbonded Distance : 2.338 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG G 192 TYR 0.086 0.009 TYR I 50 PHE 0.033 0.006 PHE C 118 TRP 0.043 0.009 TRP C 84 HIS 0.014 0.003 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.02168 / 1.13 (17697) covalent geometry : angle 1.80741 / 1.16 (24027) SS BOND : bond 0.01512 / 1.01 ( 24) SS BOND : angle 3.40602 / 2.36 ( 48) hydrogen bonds : bond 0.15410 / 10.34 ( 726) hydrogen bonds : angle 7.61563 / 5.53 ( 2070) link_BETA1-4 : bond 0.07326 / 3.67 ( 3) link_BETA1-4 : angle 4.69417 / 2.09 ( 9) link_NAG-ASN : bond 0.08070 / 4.87 ( 15) link_NAG-ASN : angle 2.78795 / 1.87 ( 45) *********************** 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 : 0.699 Fit side-chains revert: symmetry clash REVERT: B 42 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7299 (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: 0.7004 (tpt) cc_final: 0.6397 (tpt) outliers start: 0 outliers final: 3 residues processed: 400 average time/residue: 0.7268 time to fit residues: 319.8268 Evaluate side-chains 199 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 196 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN L 28 ASN B 26 HIS B 46 ASN C 33 ASN D 3 GLN F 26 HIS F 46 ASN G 33 ASN G 73 ASN G 295 GLN I 60 ASN J 28 ASN K 26 HIS K 46 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.146589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121064 restraints weight = 23364.015| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.78 r_work: 0.3246 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17739 Z= 0.165 Angle : 0.718 12.421 24129 Z= 0.371 Chirality : 0.049 0.363 2625 Planarity : 0.004 0.041 3099 Dihedral : 5.683 78.477 2367 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.47 % Allowed : 8.43 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.18), residues: 2130 helix: 2.46 (0.25), residues: 360 sheet: 0.72 (0.21), residues: 579 loop : 0.32 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 81 TYR 0.029 0.002 TYR H 50 PHE 0.036 0.002 PHE A 118 TRP 0.015 0.002 TRP D 47 HIS 0.005 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (17697) covalent geometry : angle 0.70209 / 0.37 (24027) SS BOND : bond 0.00605 / 0.42 ( 24) SS BOND : angle 2.17840 / 1.37 ( 48) hydrogen bonds : bond 0.06365 / 4.29 ( 726) hydrogen bonds : angle 6.29076 / 4.61 ( 2070) link_BETA1-4 : bond 0.00502 / 0.25 ( 3) link_BETA1-4 : angle 1.83306 / 1.30 ( 9) link_NAG-ASN : bond 0.00476 / 0.31 ( 15) link_NAG-ASN : angle 2.80269 / 1.88 ( 45) *********************** 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 335 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 270 time to evaluate : 0.724 Fit side-chains REVERT: A 173 GLU cc_start: 0.6613 (tp30) cc_final: 0.6400 (tp30) REVERT: H 16 GLN cc_start: 0.8784 (mt0) cc_final: 0.8520 (mt0) REVERT: B 42 GLN cc_start: 0.6908 (mm-40) cc_final: 0.6703 (mm110) REVERT: B 105 GLU cc_start: 0.7699 (tp30) cc_final: 0.7468 (tp30) REVERT: B 125 GLN cc_start: 0.7337 (mt0) cc_final: 0.7085 (mt0) REVERT: C 285 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: D 16 GLN cc_start: 0.8939 (mt0) cc_final: 0.8625 (mt0) REVERT: D 63 LEU cc_start: 0.7905 (mt) cc_final: 0.7464 (mt) REVERT: F 69 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7955 (mm-30) REVERT: G 32 LYS cc_start: 0.8270 (mttt) cc_final: 0.7932 (ttpp) REVERT: G 145 SER cc_start: 0.8710 (m) cc_final: 0.8336 (p) REVERT: G 238 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7788 (mm-30) REVERT: G 274 MET cc_start: 0.7595 (tpt) cc_final: 0.6968 (tpt) REVERT: I 5 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7798 (mmp-170) REVERT: I 16 GLN cc_start: 0.8868 (mt0) cc_final: 0.8602 (mt0) REVERT: I 21 THR cc_start: 0.8518 (t) cc_final: 0.8275 (m) REVERT: K 125 GLN cc_start: 0.7547 (mt0) cc_final: 0.7332 (mt0) outliers start: 65 outliers final: 17 residues processed: 304 average time/residue: 0.6614 time to fit residues: 223.4332 Evaluate side-chains 202 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain H residue 18 LEU 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 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 F residue 55 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 13 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 42 optimal weight: 0.0060 chunk 93 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN B 26 HIS ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 60 ASN D 76 ASN D 105 GLN F 26 HIS F 42 GLN G 33 ASN G 199 ASN G 295 GLN I 76 ASN K 26 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115368 restraints weight = 23675.702| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.70 r_work: 0.3154 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17739 Z= 0.212 Angle : 0.703 10.139 24129 Z= 0.358 Chirality : 0.049 0.296 2625 Planarity : 0.005 0.035 3099 Dihedral : 5.447 74.388 2361 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.43 % Allowed : 10.13 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2130 helix: 2.11 (0.26), residues: 363 sheet: 0.34 (0.20), residues: 597 loop : -0.06 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 81 TYR 0.032 0.002 TYR H 50 PHE 0.030 0.002 PHE C 118 TRP 0.015 0.002 TRP D 47 HIS 0.009 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (17697) covalent geometry : angle 0.68593 / 0.35 (24027) SS BOND : bond 0.01034 / 0.70 ( 24) SS BOND : angle 2.57833 / 1.54 ( 48) hydrogen bonds : bond 0.05839 / 3.94 ( 726) hydrogen bonds : angle 5.90597 / 4.29 ( 2070) link_BETA1-4 : bond 0.00055 / 0.03 ( 3) link_BETA1-4 : angle 1.33374 / 0.73 ( 9) link_NAG-ASN : bond 0.00513 / 0.33 ( 15) link_NAG-ASN : angle 2.53616 / 1.70 ( 45) *********************** 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: 83 poor density : 220 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 111 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8830 (mm-40) REVERT: A 122 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7750 (tp30) REVERT: A 164 LEU cc_start: 0.8264 (mp) cc_final: 0.8018 (mt) REVERT: A 274 MET cc_start: 0.8350 (tpt) cc_final: 0.8119 (tpt) REVERT: H 5 ARG cc_start: 0.8182 (mmp-170) cc_final: 0.7972 (mmp-170) REVERT: H 16 GLN cc_start: 0.8886 (mt0) cc_final: 0.8641 (mt0) REVERT: H 76 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8009 (m-40) REVERT: L 22 THR cc_start: 0.8919 (m) cc_final: 0.8651 (m) REVERT: B 42 GLN cc_start: 0.6996 (mm-40) cc_final: 0.6764 (mm110) REVERT: C 127 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7412 (pt0) REVERT: C 174 LYS cc_start: 0.8833 (mttp) cc_final: 0.8463 (mttt) REVERT: C 285 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: D 16 GLN cc_start: 0.8866 (mt0) cc_final: 0.8546 (mt0) REVERT: D 53 TYR cc_start: 0.5702 (m-80) cc_final: 0.5366 (m-10) REVERT: E 24 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7786 (ttt90) REVERT: E 68 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7096 (mtp85) REVERT: G 32 LYS cc_start: 0.8228 (mttt) cc_final: 0.7989 (ttpp) REVERT: G 145 SER cc_start: 0.8677 (m) cc_final: 0.8397 (p) REVERT: G 238 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7895 (mm-30) REVERT: G 274 MET cc_start: 0.7947 (tpt) cc_final: 0.7035 (tpt) REVERT: I 5 ARG cc_start: 0.8160 (mpt180) cc_final: 0.7949 (mmp-170) REVERT: I 16 GLN cc_start: 0.8847 (mt0) cc_final: 0.8573 (mt0) REVERT: J 24 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.6901 (ttt90) REVERT: J 31 ASN cc_start: 0.8711 (p0) cc_final: 0.8504 (p0) REVERT: J 68 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8471 (mtp85) REVERT: K 72 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8496 (mttt) outliers start: 83 outliers final: 31 residues processed: 280 average time/residue: 0.6472 time to fit residues: 201.5821 Evaluate side-chains 227 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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 57 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 121 LYS 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 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 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 24 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 72 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 207 optimal weight: 9.9990 chunk 163 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 199 ASN I 76 ASN J 28 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 = 0.3826 r_free = 0.3826 target = 0.148674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124284 restraints weight = 23760.492| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.72 r_work: 0.3403 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17739 Z= 0.192 Angle : 0.664 9.600 24129 Z= 0.335 Chirality : 0.048 0.313 2625 Planarity : 0.004 0.032 3099 Dihedral : 5.266 65.859 2361 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.89 % Allowed : 12.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2130 helix: 2.00 (0.26), residues: 363 sheet: 0.25 (0.20), residues: 591 loop : -0.14 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 81 TYR 0.030 0.002 TYR H 50 PHE 0.023 0.002 PHE C 118 TRP 0.012 0.001 TRP D 47 HIS 0.005 0.001 HIS G 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (17697) covalent geometry : angle 0.64880 / 0.33 (24027) SS BOND : bond 0.00632 / 0.42 ( 24) SS BOND : angle 2.28304 / 1.26 ( 48) hydrogen bonds : bond 0.05516 / 3.72 ( 726) hydrogen bonds : angle 5.73324 / 4.16 ( 2070) link_BETA1-4 : bond 0.00054 / 0.03 ( 3) link_BETA1-4 : angle 1.08445 / 0.70 ( 9) link_NAG-ASN : bond 0.00414 / 0.26 ( 15) link_NAG-ASN : angle 2.40556 / 1.61 ( 45) *********************** 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 284 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 211 time to evaluate : 0.777 Fit side-chains REVERT: A 274 MET cc_start: 0.8293 (tpt) cc_final: 0.8042 (tpt) REVERT: H 16 GLN cc_start: 0.8956 (mt0) cc_final: 0.8648 (mt0) REVERT: L 22 THR cc_start: 0.8883 (m) cc_final: 0.8658 (m) REVERT: B 42 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6824 (mm110) REVERT: C 127 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7297 (pt0) REVERT: C 174 LYS cc_start: 0.8886 (mttp) cc_final: 0.8627 (mttt) REVERT: C 285 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: C 295 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8486 (pt0) REVERT: D 16 GLN cc_start: 0.8913 (mt0) cc_final: 0.8567 (mt0) REVERT: E 49 TYR cc_start: 0.6319 (OUTLIER) cc_final: 0.6081 (t80) REVERT: E 68 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7178 (mtp85) REVERT: G 145 SER cc_start: 0.8694 (m) cc_final: 0.8459 (p) REVERT: G 238 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7987 (mm-30) REVERT: G 274 MET cc_start: 0.7928 (tpt) cc_final: 0.6918 (tpt) REVERT: I 16 GLN cc_start: 0.8896 (mt0) cc_final: 0.8577 (mt0) REVERT: I 38 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8263 (ptt180) REVERT: K 72 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8487 (mttt) outliers start: 73 outliers final: 29 residues processed: 267 average time/residue: 0.6382 time to fit residues: 189.7507 Evaluate side-chains 223 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain H residue 18 LEU 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 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 121 LYS 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 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain G residue 80 ILE 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 38 ARG 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 44 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 196 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.0040 chunk 111 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 178 optimal weight: 0.4980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 60 ASN H 76 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 3 GLN D 60 ASN D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN I 76 ASN J 28 ASN K 26 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130783 restraints weight = 23973.190| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.93 r_work: 0.3381 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17739 Z= 0.121 Angle : 0.585 9.501 24129 Z= 0.297 Chirality : 0.045 0.291 2625 Planarity : 0.004 0.031 3099 Dihedral : 4.983 66.265 2361 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.20 % Allowed : 14.45 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2130 helix: 2.13 (0.26), residues: 363 sheet: 0.16 (0.22), residues: 522 loop : -0.16 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 81 TYR 0.024 0.001 TYR H 50 PHE 0.015 0.001 PHE C 118 TRP 0.008 0.001 TRP D 47 HIS 0.007 0.001 HIS K 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (17697) covalent geometry : angle 0.57049 / 0.29 (24027) SS BOND : bond 0.00480 / 0.33 ( 24) SS BOND : angle 2.19163 / 1.27 ( 48) hydrogen bonds : bond 0.04860 / 3.28 ( 726) hydrogen bonds : angle 5.46458 / 3.97 ( 2070) link_BETA1-4 : bond 0.00245 / 0.12 ( 3) link_BETA1-4 : angle 0.88445 / 0.59 ( 9) link_NAG-ASN : bond 0.00378 / 0.24 ( 15) link_NAG-ASN : angle 2.06588 / 1.39 ( 45) *********************** 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 269 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 209 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8949 (mm-40) REVERT: A 122 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: H 16 GLN cc_start: 0.8949 (mt0) cc_final: 0.8636 (mt0) REVERT: L 22 THR cc_start: 0.8867 (m) cc_final: 0.8636 (m) REVERT: C 174 LYS cc_start: 0.8873 (mttp) cc_final: 0.8630 (mttt) REVERT: C 285 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: D 16 GLN cc_start: 0.8907 (mt0) cc_final: 0.8559 (mt0) REVERT: E 68 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7049 (mtp85) REVERT: G 32 LYS cc_start: 0.8302 (mttt) cc_final: 0.8043 (ttpp) REVERT: G 78 LEU cc_start: 0.8728 (mm) cc_final: 0.8496 (tt) REVERT: G 145 SER cc_start: 0.8697 (m) cc_final: 0.8457 (p) REVERT: G 219 LYS cc_start: 0.8281 (tptt) cc_final: 0.7819 (tppp) REVERT: G 238 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8057 (mm-30) REVERT: G 274 MET cc_start: 0.7906 (tpt) cc_final: 0.6872 (tpt) REVERT: I 16 GLN cc_start: 0.8885 (mt0) cc_final: 0.8558 (mt0) REVERT: J 4 MET cc_start: 0.8509 (mmm) cc_final: 0.8084 (mmm) outliers start: 60 outliers final: 21 residues processed: 250 average time/residue: 0.6345 time to fit residues: 176.1614 Evaluate side-chains 219 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 58 THR 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 56 ILE 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 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain G residue 77 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 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 33 ASN I 76 ASN 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 = 0.3842 r_free = 0.3842 target = 0.149927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124994 restraints weight = 23636.360| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.85 r_work: 0.3389 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17739 Z= 0.157 Angle : 0.613 9.570 24129 Z= 0.308 Chirality : 0.046 0.298 2625 Planarity : 0.004 0.028 3099 Dihedral : 4.991 66.708 2361 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.89 % Allowed : 14.08 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.18), residues: 2130 helix: 2.06 (0.26), residues: 363 sheet: 0.14 (0.22), residues: 522 loop : -0.20 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 81 TYR 0.033 0.002 TYR D 50 PHE 0.021 0.002 PHE C 118 TRP 0.010 0.001 TRP I 35A HIS 0.005 0.001 HIS K 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (17697) covalent geometry : angle 0.59954 / 0.30 (24027) SS BOND : bond 0.00554 / 0.37 ( 24) SS BOND : angle 2.06714 / 1.15 ( 48) hydrogen bonds : bond 0.04942 / 3.35 ( 726) hydrogen bonds : angle 5.45007 / 3.95 ( 2070) link_BETA1-4 : bond 0.00058 / 0.03 ( 3) link_BETA1-4 : angle 0.91380 / 0.57 ( 9) link_NAG-ASN : bond 0.00370 / 0.23 ( 15) link_NAG-ASN : angle 2.17976 / 1.45 ( 45) *********************** 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 281 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 208 time to evaluate : 0.673 Fit side-chains REVERT: H 16 GLN cc_start: 0.8957 (mt0) cc_final: 0.8627 (mt0) REVERT: H 17 THR cc_start: 0.8519 (p) cc_final: 0.8258 (t) REVERT: H 37 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7885 (pt) REVERT: L 22 THR cc_start: 0.8865 (m) cc_final: 0.8645 (m) REVERT: B 57 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: C 127 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7503 (pt0) REVERT: C 174 LYS cc_start: 0.8883 (mttp) cc_final: 0.8671 (mtpt) REVERT: D 16 GLN cc_start: 0.8915 (mt0) cc_final: 0.8549 (mt0) REVERT: D 37 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7841 (mt) REVERT: E 49 TYR cc_start: 0.6056 (OUTLIER) cc_final: 0.5778 (t80) REVERT: E 68 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7204 (mtp85) REVERT: G 78 LEU cc_start: 0.8777 (mm) cc_final: 0.8520 (tt) REVERT: G 145 SER cc_start: 0.8690 (m) cc_final: 0.8472 (p) REVERT: G 238 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8101 (mm-30) REVERT: G 274 MET cc_start: 0.7948 (tpt) cc_final: 0.6945 (tpt) REVERT: I 5 ARG cc_start: 0.7880 (mmp-170) cc_final: 0.7534 (mmp-170) REVERT: I 16 GLN cc_start: 0.8894 (mt0) cc_final: 0.8553 (mt0) REVERT: I 37 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8102 (pt) REVERT: I 38 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8300 (ptt180) outliers start: 73 outliers final: 28 residues processed: 258 average time/residue: 0.5635 time to fit residues: 161.8600 Evaluate side-chains 228 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR 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 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 L residue 14 SER 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 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 D residue 21 THR Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 121 LYS 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 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 38 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 137 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 60 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 60 ASN D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN K 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.145230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120344 restraints weight = 23684.667| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.85 r_work: 0.3328 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 17739 Z= 0.285 Angle : 0.736 10.907 24129 Z= 0.371 Chirality : 0.050 0.422 2625 Planarity : 0.005 0.039 3099 Dihedral : 5.330 66.554 2361 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.89 % Allowed : 14.45 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2130 helix: 1.85 (0.26), residues: 363 sheet: -0.02 (0.22), residues: 528 loop : -0.41 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 81 TYR 0.041 0.003 TYR D 50 PHE 0.027 0.002 PHE C 118 TRP 0.012 0.002 TRP I 35A HIS 0.007 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.28 (17697) covalent geometry : angle 0.72161 / 0.37 (24027) SS BOND : bond 0.00822 / 0.55 ( 24) SS BOND : angle 2.49987 / 1.30 ( 48) hydrogen bonds : bond 0.05526 / 3.74 ( 726) hydrogen bonds : angle 5.73317 / 4.15 ( 2070) link_BETA1-4 : bond 0.00212 / 0.10 ( 3) link_BETA1-4 : angle 0.96649 / 0.56 ( 9) link_NAG-ASN : bond 0.00436 / 0.26 ( 15) link_NAG-ASN : angle 2.42889 / 1.61 ( 45) *********************** 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 282 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 209 time to evaluate : 0.632 Fit side-chains REVERT: H 16 GLN cc_start: 0.8913 (mt0) cc_final: 0.8596 (mt0) REVERT: H 37 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8145 (pt) REVERT: L 22 THR cc_start: 0.8978 (m) cc_final: 0.8765 (m) REVERT: B 57 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: C 127 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: D 16 GLN cc_start: 0.8891 (mt0) cc_final: 0.8493 (mt0) REVERT: D 37 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7838 (mt) REVERT: E 68 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7319 (mtp85) REVERT: G 78 LEU cc_start: 0.8783 (mm) cc_final: 0.8560 (tt) REVERT: G 219 LYS cc_start: 0.8419 (tptt) cc_final: 0.7983 (tppp) REVERT: G 274 MET cc_start: 0.8061 (tpt) cc_final: 0.6956 (tpt) REVERT: I 16 GLN cc_start: 0.8922 (mt0) cc_final: 0.8588 (mt0) REVERT: I 38 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8272 (ptt180) REVERT: I 64 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6550 (ttp80) REVERT: J 4 MET cc_start: 0.8568 (mmm) cc_final: 0.8070 (mmm) REVERT: J 68 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8075 (mtp85) REVERT: K 72 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8510 (mttt) outliers start: 73 outliers final: 38 residues processed: 259 average time/residue: 0.5728 time to fit residues: 165.6819 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 : 0.812 ------------------------------------------------------------------------------- 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 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 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 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 D residue 21 THR Chi-restraints excluded: chain D residue 37 ILE 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 48 ILE Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 145 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 54 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 199 ASN D 3 GLN D 76 ASN F 26 HIS J 28 ASN 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 = 0.3857 r_free = 0.3857 target = 0.151283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125765 restraints weight = 23805.493| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.88 r_work: 0.3356 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17739 Z= 0.146 Angle : 0.616 10.045 24129 Z= 0.310 Chirality : 0.046 0.318 2625 Planarity : 0.004 0.032 3099 Dihedral : 5.127 68.363 2361 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.20 % Allowed : 16.11 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2130 helix: 1.98 (0.26), residues: 363 sheet: 0.44 (0.23), residues: 462 loop : -0.43 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 81 TYR 0.031 0.002 TYR I 50 PHE 0.015 0.001 PHE A 118 TRP 0.009 0.001 TRP D 47 HIS 0.004 0.001 HIS K 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (17697) covalent geometry : angle 0.60311 / 0.31 (24027) SS BOND : bond 0.00525 / 0.36 ( 24) SS BOND : angle 2.06632 / 1.07 ( 48) hydrogen bonds : bond 0.04883 / 3.31 ( 726) hydrogen bonds : angle 5.52338 / 4.01 ( 2070) link_BETA1-4 : bond 0.00079 / 0.04 ( 3) link_BETA1-4 : angle 0.88137 / 0.55 ( 9) link_NAG-ASN : bond 0.00303 / 0.19 ( 15) link_NAG-ASN : angle 2.06914 / 1.38 ( 45) *********************** 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 270 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 0.697 Fit side-chains REVERT: H 16 GLN cc_start: 0.8917 (mt0) cc_final: 0.8583 (mt0) REVERT: L 22 THR cc_start: 0.8904 (m) cc_final: 0.8687 (m) REVERT: C 127 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: D 16 GLN cc_start: 0.8901 (mt0) cc_final: 0.8508 (mt0) REVERT: D 37 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7869 (mt) REVERT: D 53 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7527 (p90) REVERT: E 68 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7237 (mtp85) REVERT: G 32 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8181 (ttpp) REVERT: G 219 LYS cc_start: 0.8329 (tptt) cc_final: 0.7893 (tppp) REVERT: G 238 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8060 (mm-30) REVERT: G 274 MET cc_start: 0.7955 (tpt) cc_final: 0.6801 (tpt) REVERT: I 5 ARG cc_start: 0.7955 (mmp-170) cc_final: 0.7604 (mmp-170) REVERT: I 16 GLN cc_start: 0.8878 (mt0) cc_final: 0.8528 (mt0) REVERT: J 4 MET cc_start: 0.8563 (mmm) cc_final: 0.8071 (mmm) REVERT: J 18 ARG cc_start: 0.8076 (ttt180) cc_final: 0.7801 (mtp180) REVERT: J 68 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8380 (ptm-80) outliers start: 60 outliers final: 28 residues processed: 250 average time/residue: 0.6020 time to fit residues: 168.2961 Evaluate side-chains 228 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 50 TYR 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 121 LYS 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 37 ILE Chi-restraints excluded: chain D residue 53 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 121 LYS 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 6 GLU 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 J residue 68 ARG Chi-restraints excluded: chain K residue 121 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 60 ASN B 26 HIS C 199 ASN D 3 GLN D 54 ASN D 60 ASN D 76 ASN ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 ASN J 28 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120834 restraints weight = 23754.396| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.78 r_work: 0.3361 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17739 Z= 0.204 Angle : 0.671 10.532 24129 Z= 0.336 Chirality : 0.047 0.339 2625 Planarity : 0.004 0.031 3099 Dihedral : 5.248 69.097 2361 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.72 % Allowed : 16.64 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2130 helix: 1.88 (0.26), residues: 363 sheet: 0.45 (0.23), residues: 462 loop : -0.51 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 81 TYR 0.038 0.002 TYR E 49 PHE 0.021 0.002 PHE C 118 TRP 0.010 0.002 TRP I 35A HIS 0.004 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.20 (17697) covalent geometry : angle 0.65608 / 0.33 (24027) SS BOND : bond 0.00653 / 0.44 ( 24) SS BOND : angle 2.45499 / 1.42 ( 48) hydrogen bonds : bond 0.05099 / 3.46 ( 726) hydrogen bonds : angle 5.62146 / 4.07 ( 2070) link_BETA1-4 : bond 0.00019 / 0.01 ( 3) link_BETA1-4 : angle 0.83688 / 0.50 ( 9) link_NAG-ASN : bond 0.00339 / 0.21 ( 15) link_NAG-ASN : angle 2.19752 / 1.46 ( 45) *********************** 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 255 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 204 time to evaluate : 0.608 Fit side-chains REVERT: H 16 GLN cc_start: 0.8931 (mt0) cc_final: 0.8578 (mt0) REVERT: L 22 THR cc_start: 0.8903 (m) cc_final: 0.8688 (m) REVERT: B 116 LYS cc_start: 0.8114 (mttt) cc_final: 0.7432 (mptt) REVERT: C 127 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7235 (pt0) REVERT: D 5 ARG cc_start: 0.7789 (mmp-170) cc_final: 0.7511 (mmp-170) REVERT: D 16 GLN cc_start: 0.8872 (mt0) cc_final: 0.8459 (mt0) REVERT: D 37 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7843 (mt) REVERT: E 68 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7180 (mtp85) REVERT: G 32 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8100 (ttpp) REVERT: G 219 LYS cc_start: 0.8286 (tptt) cc_final: 0.7864 (tppp) REVERT: G 274 MET cc_start: 0.7947 (tpt) cc_final: 0.6862 (tpt) REVERT: G 316 MET cc_start: 0.8502 (ttm) cc_final: 0.8287 (mtt) REVERT: I 5 ARG cc_start: 0.7939 (mmp-170) cc_final: 0.7578 (mmp-170) REVERT: I 16 GLN cc_start: 0.8882 (mt0) cc_final: 0.8545 (mt0) REVERT: J 4 MET cc_start: 0.8554 (mmm) cc_final: 0.8063 (mmm) REVERT: J 18 ARG cc_start: 0.8045 (ttt180) cc_final: 0.7776 (mtp180) REVERT: J 68 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7928 (mtp85) outliers start: 51 outliers final: 37 residues processed: 240 average time/residue: 0.5636 time to fit residues: 151.6115 Evaluate side-chains 236 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 121 LYS 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 37 ILE 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 48 ILE Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 121 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 54 ASN H 60 ASN B 26 HIS C 33 ASN C 199 ASN D 3 GLN D 54 ASN D 76 ASN ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.152234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126770 restraints weight = 23797.667| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.88 r_work: 0.3343 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17739 Z= 0.137 Angle : 0.606 9.706 24129 Z= 0.306 Chirality : 0.045 0.263 2625 Planarity : 0.004 0.033 3099 Dihedral : 5.110 70.320 2361 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.35 % Allowed : 17.39 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 2130 helix: 1.93 (0.26), residues: 363 sheet: 0.48 (0.24), residues: 462 loop : -0.47 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 81 TYR 0.037 0.002 TYR L 49 PHE 0.015 0.001 PHE A 118 TRP 0.009 0.001 TRP B 92 HIS 0.004 0.001 HIS K 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (17697) covalent geometry : angle 0.59242 / 0.30 (24027) SS BOND : bond 0.00514 / 0.35 ( 24) SS BOND : angle 2.28587 / 1.33 ( 48) hydrogen bonds : bond 0.04714 / 3.20 ( 726) hydrogen bonds : angle 5.46000 / 3.96 ( 2070) link_BETA1-4 : bond 0.00097 / 0.05 ( 3) link_BETA1-4 : angle 0.82948 / 0.52 ( 9) link_NAG-ASN : bond 0.00301 / 0.19 ( 15) link_NAG-ASN : angle 1.99803 / 1.33 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: H 16 GLN cc_start: 0.8922 (mt0) cc_final: 0.8580 (mt0) REVERT: L 22 THR cc_start: 0.8832 (m) cc_final: 0.8616 (m) REVERT: L 68 ARG cc_start: 0.8683 (mtp85) cc_final: 0.8094 (ptm160) REVERT: B 116 LYS cc_start: 0.7960 (mttt) cc_final: 0.7335 (mptt) REVERT: C 127 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7384 (pt0) REVERT: D 5 ARG cc_start: 0.7751 (mmp-170) cc_final: 0.7484 (mmp-170) REVERT: D 16 GLN cc_start: 0.8855 (mt0) cc_final: 0.8463 (mt0) REVERT: D 37 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7914 (mt) REVERT: E 68 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7139 (mtp85) REVERT: F 116 LYS cc_start: 0.8307 (mttt) cc_final: 0.7668 (mptt) REVERT: G 219 LYS cc_start: 0.8274 (tptt) cc_final: 0.7838 (tppp) REVERT: G 274 MET cc_start: 0.7884 (tpt) cc_final: 0.6790 (tpt) REVERT: G 316 MET cc_start: 0.8514 (ttm) cc_final: 0.8293 (mtt) REVERT: I 5 ARG cc_start: 0.7948 (mmp-170) cc_final: 0.7588 (mmp-170) REVERT: I 16 GLN cc_start: 0.8804 (mt0) cc_final: 0.8427 (mt0) REVERT: J 4 MET cc_start: 0.8556 (mmm) cc_final: 0.8191 (mmm) REVERT: J 68 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8317 (ptm-80) outliers start: 44 outliers final: 30 residues processed: 243 average time/residue: 0.6475 time to fit residues: 174.8188 Evaluate side-chains 236 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain B residue 55 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 37 ILE 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 G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 121 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 96 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 ASN H 60 ASN L 3 GLN B 26 HIS C 199 ASN D 3 GLN D 54 ASN D 60 ASN D 76 ASN ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 ASN I 100EASN J 28 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124181 restraints weight = 23857.440| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.89 r_work: 0.3316 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17739 Z= 0.214 Angle : 0.676 9.966 24129 Z= 0.339 Chirality : 0.048 0.336 2625 Planarity : 0.004 0.033 3099 Dihedral : 5.290 70.857 2361 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.56 % Allowed : 17.23 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2130 helix: 1.92 (0.26), residues: 363 sheet: 0.43 (0.23), residues: 462 loop : -0.57 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 81 TYR 0.043 0.002 TYR E 49 PHE 0.021 0.002 PHE C 118 TRP 0.011 0.002 TRP H 35A HIS 0.006 0.001 HIS K 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.21 (17697) covalent geometry : angle 0.66218 / 0.33 (24027) SS BOND : bond 0.00665 / 0.45 ( 24) SS BOND : angle 2.39769 / 1.38 ( 48) hydrogen bonds : bond 0.05057 / 3.44 ( 726) hydrogen bonds : angle 5.59426 / 4.05 ( 2070) link_BETA1-4 : bond 0.00069 / 0.03 ( 3) link_BETA1-4 : angle 0.79808 / 0.47 ( 9) link_NAG-ASN : bond 0.00334 / 0.20 ( 15) link_NAG-ASN : angle 2.14696 / 1.42 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5976.28 seconds wall clock time: 102 minutes 54.20 seconds (6174.20 seconds total)