Starting phenix.real_space_refine on Sun Aug 24 05:24:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tpa_41471/08_2025/8tpa_41471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tpa_41471/08_2025/8tpa_41471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tpa_41471/08_2025/8tpa_41471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tpa_41471/08_2025/8tpa_41471.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tpa_41471/08_2025/8tpa_41471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tpa_41471/08_2025/8tpa_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: C, G, D, I, E, J, F, K, N, O Time building chain proxies: 2.51, per 1000 atoms: 0.15 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: 1.15 Conformation dependent library (CDL) restraints added in 590.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.76 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: 2.90 Time building geometry restraints manager: 1.57 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: 10329 17.80 - 35.61: 273 35.61 - 53.41: 109 53.41 - 71.22: 38 71.22 - 89.02: 9 Dihedral angle restraints: 10758 sinusoidal: 4539 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 10755 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: 0.03 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: 2.580 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:8.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.152 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 : 10.431 89.023 6726 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 aren 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 covalent geometry : bond 0.02168 (17697) covalent geometry : angle 1.80741 (24027) SS BOND : bond 0.01512 ( 24) SS BOND : angle 3.40602 ( 48) hydrogen bonds : bond 0.15410 ( 726) hydrogen bonds : angle 7.61563 ( 2070) link_BETA1-4 : bond 0.07326 ( 3) link_BETA1-4 : angle 4.69417 ( 9) link_NAG-ASN : bond 0.08070 ( 15) link_NAG-ASN : angle 2.78795 ( 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 : 0.656 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: 0.7003 (tpt) cc_final: 0.6397 (tpt) outliers start: 0 outliers final: 3 residues processed: 400 average time/residue: 0.6848 time to fit residues: 299.8588 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 : 0.570 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 33 ASN L 28 ASN B 26 HIS B 46 ASN C 33 ASN D 3 GLN F 26 HIS F 42 GLN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121193 restraints weight = 23354.037| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.86 r_work: 0.3247 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17739 Z= 0.162 Angle : 0.721 12.861 24129 Z= 0.374 Chirality : 0.049 0.362 2625 Planarity : 0.004 0.041 3099 Dihedral : 6.410 79.344 2745 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.36 % Allowed : 8.53 % 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 aren not related in a simple way. whole: 1.19 (0.18), residues: 2130 helix: 2.55 (0.25), residues: 360 sheet: 0.77 (0.21), residues: 579 loop : 0.34 (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 0.035 0.002 PHE C 118 TRP 0.015 0.002 TRP D 47 HIS 0.006 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00359 (17697) covalent geometry : angle 0.70474 (24027) SS BOND : bond 0.00689 ( 24) SS BOND : angle 2.13973 ( 48) hydrogen bonds : bond 0.06554 ( 726) hydrogen bonds : angle 6.34116 ( 2070) link_BETA1-4 : bond 0.00310 ( 3) link_BETA1-4 : angle 1.59784 ( 9) link_NAG-ASN : bond 0.00455 ( 15) link_NAG-ASN : angle 2.91078 ( 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 321 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 258 time to evaluate : 0.564 Fit side-chains REVERT: A 173 GLU cc_start: 0.6651 (tp30) cc_final: 0.6438 (tp30) REVERT: H 16 GLN cc_start: 0.8748 (mt0) cc_final: 0.8502 (mt0) REVERT: H 72 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: B 105 GLU cc_start: 0.7688 (tp30) cc_final: 0.7461 (tp30) REVERT: B 125 GLN cc_start: 0.7346 (mt0) cc_final: 0.7100 (mt0) REVERT: C 60 GLN cc_start: 0.8752 (mt0) cc_final: 0.8526 (mt0) REVERT: C 285 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: D 16 GLN cc_start: 0.8970 (mt0) cc_final: 0.8714 (mt0) REVERT: D 63 LEU cc_start: 0.7922 (mt) cc_final: 0.7486 (mt) REVERT: F 69 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7984 (mm-30) REVERT: G 32 LYS cc_start: 0.8264 (mttt) cc_final: 0.7889 (ttpp) REVERT: G 145 SER cc_start: 0.8774 (m) cc_final: 0.8394 (p) REVERT: G 238 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7734 (mm-30) REVERT: G 261 SER cc_start: 0.9100 (t) cc_final: 0.8826 (m) REVERT: G 274 MET cc_start: 0.7585 (tpt) cc_final: 0.6779 (tpt) REVERT: I 5 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7790 (mmp-170) REVERT: I 16 GLN cc_start: 0.8879 (mt0) cc_final: 0.8641 (mt0) REVERT: I 21 THR cc_start: 0.8501 (t) cc_final: 0.8247 (m) outliers start: 63 outliers final: 17 residues processed: 290 average time/residue: 0.6103 time to fit residues: 195.7124 Evaluate side-chains 204 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 78 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 72 GLU 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 70 SER Chi-restraints excluded: chain D residue 98 VAL 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 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: 3.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 42 optimal weight: 0.0670 chunk 93 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN B 26 HIS D 76 ASN D 105 GLN F 26 HIS G 33 ASN G 199 ASN G 295 GLN I 76 ASN K 26 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117998 restraints weight = 23615.094| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.76 r_work: 0.3202 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2995 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 : 0.657 9.598 24129 Z= 0.336 Chirality : 0.048 0.273 2625 Planarity : 0.004 0.036 3099 Dihedral : 5.914 75.850 2739 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.37 % Allowed : 9.97 % Favored : 85.65 % 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 aren not related in a simple way. whole: 0.76 (0.18), residues: 2130 helix: 2.17 (0.26), residues: 363 sheet: 0.50 (0.21), residues: 579 loop : 0.05 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 81 TYR 0.031 0.002 TYR H 50 PHE 0.027 0.002 PHE C 118 TRP 0.014 0.001 TRP D 47 HIS 0.007 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00381 (17697) covalent geometry : angle 0.64002 (24027) SS BOND : bond 0.00652 ( 24) SS BOND : angle 2.40034 ( 48) hydrogen bonds : bond 0.05617 ( 726) hydrogen bonds : angle 5.82696 ( 2070) link_BETA1-4 : bond 0.00311 ( 3) link_BETA1-4 : angle 1.26952 ( 9) link_NAG-ASN : bond 0.00501 ( 15) link_NAG-ASN : angle 2.45912 ( 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 312 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 230 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7899 (tp30) REVERT: A 164 LEU cc_start: 0.8188 (mp) cc_final: 0.7912 (mt) REVERT: A 174 LYS cc_start: 0.8577 (mttp) cc_final: 0.8366 (mtpt) REVERT: H 5 ARG cc_start: 0.8178 (mmp-170) cc_final: 0.7976 (mmp-170) REVERT: H 16 GLN cc_start: 0.8839 (mt0) cc_final: 0.8558 (mt0) REVERT: L 22 THR cc_start: 0.8923 (m) cc_final: 0.8670 (m) REVERT: C 127 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: C 174 LYS cc_start: 0.8776 (mttp) cc_final: 0.8353 (mttt) REVERT: C 285 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: D 16 GLN cc_start: 0.8934 (mt0) cc_final: 0.8624 (mt0) REVERT: D 53 TYR cc_start: 0.5709 (m-80) cc_final: 0.5430 (m-10) REVERT: E 24 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7681 (ttt90) REVERT: F 69 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8046 (mm-30) REVERT: G 32 LYS cc_start: 0.8242 (mttt) cc_final: 0.7915 (ttpp) REVERT: G 145 SER cc_start: 0.8687 (m) cc_final: 0.8371 (p) REVERT: G 238 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7908 (mm-30) REVERT: G 274 MET cc_start: 0.7831 (tpt) cc_final: 0.6901 (tpt) REVERT: I 16 GLN cc_start: 0.8822 (mt0) cc_final: 0.8543 (mt0) REVERT: J 24 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.6955 (ttt90) REVERT: J 68 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8453 (mtp85) REVERT: K 72 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8531 (mttt) outliers start: 82 outliers final: 29 residues processed: 288 average time/residue: 0.5520 time to fit residues: 176.9179 Evaluate side-chains 225 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 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 51 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 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 E residue 5 THR Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain G residue 27 ASP 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 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: 3.9990 chunk 26 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS C 33 ASN D 60 ASN D 76 ASN D 105 GLN F 26 HIS 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 = 0.3855 r_free = 0.3855 target = 0.150947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125983 restraints weight = 23711.712| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.83 r_work: 0.3414 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17739 Z= 0.154 Angle : 0.619 9.623 24129 Z= 0.313 Chirality : 0.047 0.304 2625 Planarity : 0.004 0.031 3099 Dihedral : 5.667 64.069 2739 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.73 % Allowed : 12.43 % Favored : 83.84 % 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 aren not related in a simple way. whole: 0.53 (0.18), residues: 2130 helix: 2.07 (0.26), residues: 363 sheet: 0.23 (0.22), residues: 522 loop : -0.05 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 81 TYR 0.030 0.002 TYR I 50 PHE 0.023 0.002 PHE C 118 TRP 0.010 0.001 TRP D 47 HIS 0.005 0.001 HIS G 47 Details of bonding type rmsd covalent geometry : bond 0.00360 (17697) covalent geometry : angle 0.60354 (24027) SS BOND : bond 0.00682 ( 24) SS BOND : angle 2.23620 ( 48) hydrogen bonds : bond 0.05253 ( 726) hydrogen bonds : angle 5.60996 ( 2070) link_BETA1-4 : bond 0.00176 ( 3) link_BETA1-4 : angle 1.12580 ( 9) link_NAG-ASN : bond 0.00387 ( 15) link_NAG-ASN : angle 2.31957 ( 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 278 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 208 time to evaluate : 0.693 Fit side-chains REVERT: H 16 GLN cc_start: 0.8919 (mt0) cc_final: 0.8640 (mt0) REVERT: H 76 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.7935 (m-40) REVERT: L 22 THR cc_start: 0.8948 (m) cc_final: 0.8714 (m) REVERT: C 127 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7351 (pt0) REVERT: C 174 LYS cc_start: 0.8838 (mttp) cc_final: 0.8546 (mttt) REVERT: C 285 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: D 16 GLN cc_start: 0.8928 (mt0) cc_final: 0.8584 (mt0) REVERT: D 53 TYR cc_start: 0.5635 (m-80) cc_final: 0.5314 (m-80) REVERT: G 145 SER cc_start: 0.8682 (m) cc_final: 0.8424 (p) REVERT: G 238 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7977 (mm-30) REVERT: G 274 MET cc_start: 0.7769 (tpt) cc_final: 0.6887 (tpt) REVERT: I 16 GLN cc_start: 0.8868 (mt0) cc_final: 0.8559 (mt0) REVERT: J 4 MET cc_start: 0.8540 (mmm) cc_final: 0.8153 (mmm) REVERT: J 31 ASN cc_start: 0.8740 (p0) cc_final: 0.8501 (p0) REVERT: K 72 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8488 (mttt) outliers start: 70 outliers final: 29 residues processed: 257 average time/residue: 0.6087 time to fit residues: 173.8200 Evaluate side-chains 221 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 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 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 142 HIS 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 261 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 70 SER Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain G residue 261 SER 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 I residue 76 ASN Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 72 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 196 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 178 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 76 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 60 ASN D 76 ASN F 26 HIS G 199 ASN I 76 ASN 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 = 0.3868 r_free = 0.3868 target = 0.152032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127857 restraints weight = 23642.177| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.75 r_work: 0.3392 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17739 Z= 0.135 Angle : 0.601 9.557 24129 Z= 0.304 Chirality : 0.045 0.324 2625 Planarity : 0.004 0.030 3099 Dihedral : 5.570 65.094 2739 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.25 % Allowed : 13.60 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.18), residues: 2130 helix: 2.11 (0.26), residues: 363 sheet: 0.19 (0.22), residues: 522 loop : -0.10 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 81 TYR 0.031 0.002 TYR B 162 PHE 0.018 0.002 PHE C 118 TRP 0.010 0.001 TRP H 35A HIS 0.013 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00311 (17697) covalent geometry : angle 0.58603 (24027) SS BOND : bond 0.00505 ( 24) SS BOND : angle 2.24271 ( 48) hydrogen bonds : bond 0.04992 ( 726) hydrogen bonds : angle 5.48865 ( 2070) link_BETA1-4 : bond 0.00210 ( 3) link_BETA1-4 : angle 1.05897 ( 9) link_NAG-ASN : bond 0.00350 ( 15) link_NAG-ASN : angle 2.20300 ( 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 271 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 210 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.8907 (mt0) cc_final: 0.8594 (mt0) REVERT: L 22 THR cc_start: 0.8869 (m) cc_final: 0.8639 (m) REVERT: C 127 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: C 174 LYS cc_start: 0.8845 (mttp) cc_final: 0.8580 (mttt) REVERT: C 285 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: C 295 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8468 (pt0) REVERT: D 16 GLN cc_start: 0.8899 (mt0) cc_final: 0.8547 (mt0) REVERT: E 68 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7382 (mtp85) REVERT: G 145 SER cc_start: 0.8658 (m) cc_final: 0.8410 (p) REVERT: G 238 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7943 (mm-30) REVERT: G 274 MET cc_start: 0.7779 (tpt) cc_final: 0.6776 (tpt) REVERT: I 16 GLN cc_start: 0.8848 (mt0) cc_final: 0.8505 (mt0) REVERT: J 31 ASN cc_start: 0.8844 (p0) cc_final: 0.8604 (p0) REVERT: K 72 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8441 (mttt) outliers start: 61 outliers final: 30 residues processed: 254 average time/residue: 0.6305 time to fit residues: 177.3886 Evaluate side-chains 230 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 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 B residue 57 GLU 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 18 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 49 TYR 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 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 K residue 72 LYS Chi-restraints excluded: chain K residue 121 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.0670 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 76 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN D 60 ASN D 76 ASN E 79 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.155155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130042 restraints weight = 23889.891| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.91 r_work: 0.3408 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3733 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= 0.130 Angle : 0.587 9.561 24129 Z= 0.295 Chirality : 0.045 0.314 2625 Planarity : 0.004 0.031 3099 Dihedral : 5.459 66.415 2739 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.52 % Allowed : 13.97 % Favored : 82.51 % 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 aren not related in a simple way. whole: 0.49 (0.18), residues: 2130 helix: 2.19 (0.26), residues: 363 sheet: 0.21 (0.22), residues: 522 loop : -0.13 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 81 TYR 0.029 0.002 TYR D 100G PHE 0.018 0.001 PHE C 118 TRP 0.015 0.001 TRP D 103 HIS 0.007 0.001 HIS K 26 Details of bonding type rmsd covalent geometry : bond 0.00297 (17697) covalent geometry : angle 0.57457 (24027) SS BOND : bond 0.00496 ( 24) SS BOND : angle 1.96595 ( 48) hydrogen bonds : bond 0.04755 ( 726) hydrogen bonds : angle 5.39224 ( 2070) link_BETA1-4 : bond 0.00208 ( 3) link_BETA1-4 : angle 0.98280 ( 9) link_NAG-ASN : bond 0.00330 ( 15) link_NAG-ASN : angle 2.09978 ( 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: 66 poor density : 215 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7415 (pt0) cc_final: 0.7126 (tp30) REVERT: H 16 GLN cc_start: 0.8913 (mt0) cc_final: 0.8575 (mt0) REVERT: C 127 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: D 16 GLN cc_start: 0.8915 (mt0) cc_final: 0.8576 (mt0) REVERT: E 68 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7469 (mtp85) REVERT: E 79 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7637 (mt0) REVERT: G 145 SER cc_start: 0.8684 (m) cc_final: 0.8454 (p) REVERT: G 238 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8027 (mm-30) REVERT: G 274 MET cc_start: 0.7865 (tpt) cc_final: 0.6871 (tpt) REVERT: I 16 GLN cc_start: 0.8795 (mt0) cc_final: 0.8440 (mt0) REVERT: I 21 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8510 (m) REVERT: I 37 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7972 (pt) REVERT: I 76 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8281 (m-40) REVERT: J 4 MET cc_start: 0.8549 (mmm) cc_final: 0.8184 (mmm) outliers start: 66 outliers final: 26 residues processed: 259 average time/residue: 0.5345 time to fit residues: 154.0044 Evaluate side-chains 219 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 38 ARG 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 57 GLU Chi-restraints excluded: chain B residue 121 LYS 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 50 TYR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 79 GLN 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 21 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 121 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 137 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 170 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 76 ASN B 26 HIS B 142 HIS C 33 ASN C 199 ASN D 60 ASN D 76 ASN F 26 HIS I 76 ASN J 28 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.154495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129460 restraints weight = 23822.417| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.88 r_work: 0.3409 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3843 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= 0.149 Angle : 0.612 10.623 24129 Z= 0.306 Chirality : 0.046 0.338 2625 Planarity : 0.004 0.031 3099 Dihedral : 5.489 67.121 2739 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.25 % Allowed : 15.31 % Favored : 81.44 % 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 aren not related in a simple way. whole: 0.44 (0.18), residues: 2130 helix: 2.12 (0.26), residues: 363 sheet: 0.22 (0.22), residues: 522 loop : -0.18 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 81 TYR 0.030 0.002 TYR I 50 PHE 0.019 0.002 PHE C 118 TRP 0.017 0.001 TRP H 103 HIS 0.004 0.001 HIS K 26 Details of bonding type rmsd covalent geometry : bond 0.00352 (17697) covalent geometry : angle 0.59791 (24027) SS BOND : bond 0.00549 ( 24) SS BOND : angle 2.27050 ( 48) hydrogen bonds : bond 0.04788 ( 726) hydrogen bonds : angle 5.43460 ( 2070) link_BETA1-4 : bond 0.00188 ( 3) link_BETA1-4 : angle 0.97203 ( 9) link_NAG-ASN : bond 0.00322 ( 15) link_NAG-ASN : angle 2.10667 ( 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 260 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 199 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.8917 (mt0) cc_final: 0.8603 (mt0) REVERT: B 39 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6654 (pttt) REVERT: C 127 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7433 (pt0) REVERT: D 16 GLN cc_start: 0.8910 (mt0) cc_final: 0.8550 (mt0) REVERT: E 68 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7466 (mtp85) REVERT: G 119 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: G 145 SER cc_start: 0.8671 (m) cc_final: 0.8452 (p) REVERT: G 238 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8035 (mm-30) REVERT: G 274 MET cc_start: 0.7902 (tpt) cc_final: 0.6953 (tpt) REVERT: I 16 GLN cc_start: 0.8794 (mt0) cc_final: 0.8436 (mt0) REVERT: I 21 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8526 (m) REVERT: I 37 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8017 (pt) REVERT: J 4 MET cc_start: 0.8555 (mmm) cc_final: 0.8191 (mmm) REVERT: K 72 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8496 (mttt) outliers start: 61 outliers final: 34 residues processed: 242 average time/residue: 0.5179 time to fit residues: 139.6761 Evaluate side-chains 230 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 142 HIS 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 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 G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 121 LYS 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: 2.9990 chunk 124 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 76 ASN B 26 HIS B 142 HIS C 199 ASN 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 = 0.3848 r_free = 0.3848 target = 0.150443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124766 restraints weight = 23853.663| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.93 r_work: 0.3291 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17739 Z= 0.230 Angle : 0.691 16.345 24129 Z= 0.343 Chirality : 0.048 0.318 2625 Planarity : 0.005 0.032 3099 Dihedral : 5.769 67.361 2739 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.57 % Allowed : 15.04 % Favored : 81.39 % 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 aren not related in a simple way. whole: 0.29 (0.17), residues: 2130 helix: 1.92 (0.26), residues: 363 sheet: 0.27 (0.22), residues: 492 loop : -0.31 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 81 TYR 0.039 0.002 TYR J 49 PHE 0.025 0.002 PHE C 118 TRP 0.028 0.002 TRP H 103 HIS 0.028 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00556 (17697) covalent geometry : angle 0.67544 (24027) SS BOND : bond 0.00698 ( 24) SS BOND : angle 2.55956 ( 48) hydrogen bonds : bond 0.05194 ( 726) hydrogen bonds : angle 5.62374 ( 2070) link_BETA1-4 : bond 0.00040 ( 3) link_BETA1-4 : angle 1.03775 ( 9) link_NAG-ASN : bond 0.00348 ( 15) link_NAG-ASN : angle 2.26692 ( 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 265 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 198 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 GLN cc_start: 0.8910 (mt0) cc_final: 0.8584 (mt0) REVERT: L 22 THR cc_start: 0.8926 (m) cc_final: 0.8720 (m) REVERT: B 39 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6677 (pttt) REVERT: C 127 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: D 5 ARG cc_start: 0.7939 (mmp-170) cc_final: 0.7614 (mmp-170) REVERT: D 16 GLN cc_start: 0.8897 (mt0) cc_final: 0.8523 (mt0) REVERT: E 68 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7610 (mtp85) REVERT: G 119 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: G 238 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8127 (mm-30) REVERT: G 274 MET cc_start: 0.8052 (tpt) cc_final: 0.7013 (tpt) REVERT: I 16 GLN cc_start: 0.8804 (mt0) cc_final: 0.8435 (mt0) REVERT: I 21 THR cc_start: 0.8745 (t) cc_final: 0.8518 (m) REVERT: J 4 MET cc_start: 0.8591 (mmm) cc_final: 0.8198 (mmm) REVERT: K 72 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8529 (mttt) outliers start: 67 outliers final: 37 residues processed: 247 average time/residue: 0.5201 time to fit residues: 143.6951 Evaluate side-chains 235 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 70 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 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 C residue 304 GLU 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 G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 72 GLU 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 K residue 72 LYS 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: 1.9990 chunk 136 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 8 optimal weight: 0.0270 chunk 190 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 ASN H 60 ASN H 76 ASN B 26 HIS C 33 ASN 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 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 = 0.3863 r_free = 0.3863 target = 0.151799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125773 restraints weight = 23864.340| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.01 r_work: 0.3326 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17739 Z= 0.149 Angle : 0.622 13.879 24129 Z= 0.309 Chirality : 0.045 0.261 2625 Planarity : 0.004 0.033 3099 Dihedral : 5.655 68.806 2739 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.72 % Allowed : 15.95 % Favored : 81.33 % 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 aren not related in a simple way. whole: 0.36 (0.17), residues: 2130 helix: 1.96 (0.26), residues: 363 sheet: 0.54 (0.23), residues: 462 loop : -0.36 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 81 TYR 0.033 0.002 TYR J 49 PHE 0.017 0.002 PHE C 118 TRP 0.018 0.001 TRP H 103 HIS 0.004 0.001 HIS K 26 Details of bonding type rmsd covalent geometry : bond 0.00351 (17697) covalent geometry : angle 0.60793 (24027) SS BOND : bond 0.00510 ( 24) SS BOND : angle 2.28495 ( 48) hydrogen bonds : bond 0.04824 ( 726) hydrogen bonds : angle 5.51032 ( 2070) link_BETA1-4 : bond 0.00209 ( 3) link_BETA1-4 : angle 0.87585 ( 9) link_NAG-ASN : bond 0.00269 ( 15) link_NAG-ASN : angle 2.08218 ( 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 254 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: H 16 GLN cc_start: 0.8834 (mt0) cc_final: 0.8515 (mt0) REVERT: L 22 THR cc_start: 0.8882 (m) cc_final: 0.8668 (m) REVERT: B 116 LYS cc_start: 0.8026 (mttt) cc_final: 0.7320 (mptt) REVERT: C 127 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: D 5 ARG cc_start: 0.7835 (mmp-170) cc_final: 0.7564 (mmp-170) REVERT: D 16 GLN cc_start: 0.8841 (mt0) cc_final: 0.8486 (mt0) REVERT: E 68 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7631 (mtp85) REVERT: G 119 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: G 238 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8052 (mm-30) REVERT: G 274 MET cc_start: 0.7955 (tpt) cc_final: 0.6983 (tpt) REVERT: I 16 GLN cc_start: 0.8754 (mt0) cc_final: 0.8381 (mt0) REVERT: I 21 THR cc_start: 0.8772 (t) cc_final: 0.8513 (m) REVERT: J 4 MET cc_start: 0.8582 (mmm) cc_final: 0.8056 (mmm) REVERT: J 18 ARG cc_start: 0.8082 (ttt180) cc_final: 0.7789 (mtp180) REVERT: J 68 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8370 (ptm-80) REVERT: K 72 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8477 (mttt) outliers start: 51 outliers final: 33 residues processed: 237 average time/residue: 0.5373 time to fit residues: 141.9361 Evaluate side-chains 228 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 50 TYR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 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 C residue 304 GLU 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 G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 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 72 LYS 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: 7.9990 chunk 80 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN B 26 HIS C 199 ASN D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN J 28 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.152042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126466 restraints weight = 23779.889| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.92 r_work: 0.3348 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.243 17739 Z= 0.199 Angle : 0.791 59.200 24129 Z= 0.436 Chirality : 0.046 0.314 2625 Planarity : 0.004 0.033 3099 Dihedral : 5.657 68.802 2739 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.61 % Allowed : 16.27 % Favored : 81.12 % Cbeta Deviations : 0.05 % 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 aren not related in a simple way. whole: 0.35 (0.18), residues: 2130 helix: 1.95 (0.26), residues: 363 sheet: 0.54 (0.23), residues: 462 loop : -0.36 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 81 TYR 0.030 0.002 TYR I 50 PHE 0.017 0.002 PHE C 118 TRP 0.016 0.001 TRP H 103 HIS 0.004 0.001 HIS K 142 Details of bonding type rmsd covalent geometry : bond 0.00479 (17697) covalent geometry : angle 0.78096 (24027) SS BOND : bond 0.00589 ( 24) SS BOND : angle 2.23124 ( 48) hydrogen bonds : bond 0.04877 ( 726) hydrogen bonds : angle 5.51134 ( 2070) link_BETA1-4 : bond 0.00273 ( 3) link_BETA1-4 : angle 0.91223 ( 9) link_NAG-ASN : bond 0.00276 ( 15) link_NAG-ASN : angle 2.08096 ( 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 242 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: H 16 GLN cc_start: 0.8822 (mt0) cc_final: 0.8495 (mt0) REVERT: H 18 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8357 (tp) REVERT: L 22 THR cc_start: 0.8879 (m) cc_final: 0.8668 (m) REVERT: B 116 LYS cc_start: 0.8021 (mttt) cc_final: 0.7310 (mptt) REVERT: C 127 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: D 5 ARG cc_start: 0.7845 (mmp-170) cc_final: 0.7562 (mmp-170) REVERT: D 16 GLN cc_start: 0.8840 (mt0) cc_final: 0.8483 (mt0) REVERT: E 68 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7642 (mtp85) REVERT: G 119 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: G 238 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8004 (mm-30) REVERT: G 274 MET cc_start: 0.7896 (tpt) cc_final: 0.6844 (tpt) REVERT: I 16 GLN cc_start: 0.8750 (mt0) cc_final: 0.8380 (mt0) REVERT: I 21 THR cc_start: 0.8764 (t) cc_final: 0.8515 (m) REVERT: J 4 MET cc_start: 0.8570 (mmm) cc_final: 0.8196 (mmm) REVERT: J 18 ARG cc_start: 0.8082 (ttt180) cc_final: 0.7790 (mtp180) REVERT: J 68 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8371 (ptm-80) REVERT: K 72 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8478 (mttt) outliers start: 49 outliers final: 33 residues processed: 225 average time/residue: 0.5575 time to fit residues: 139.5833 Evaluate side-chains 227 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 50 TYR 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 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 C residue 304 GLU 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 G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 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 72 LYS 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: 0.8980 chunk 148 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 31 optimal weight: 0.0470 chunk 142 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS C 199 ASN D 76 ASN F 26 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.151974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126221 restraints weight = 23779.982| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.00 r_work: 0.3340 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.243 17739 Z= 0.199 Angle : 0.791 59.200 24129 Z= 0.436 Chirality : 0.046 0.314 2625 Planarity : 0.004 0.033 3099 Dihedral : 5.657 68.802 2739 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.35 % Allowed : 16.53 % Favored : 81.12 % Cbeta Deviations : 0.05 % 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 aren not related in a simple way. whole: 0.35 (0.18), residues: 2130 helix: 1.95 (0.26), residues: 363 sheet: 0.54 (0.23), residues: 462 loop : -0.36 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 81 TYR 0.030 0.002 TYR I 50 PHE 0.017 0.002 PHE C 118 TRP 0.016 0.001 TRP H 103 HIS 0.004 0.001 HIS K 142 Details of bonding type rmsd covalent geometry : bond 0.00479 (17697) covalent geometry : angle 0.78096 (24027) SS BOND : bond 0.00589 ( 24) SS BOND : angle 2.23124 ( 48) hydrogen bonds : bond 0.04877 ( 726) hydrogen bonds : angle 5.51134 ( 2070) link_BETA1-4 : bond 0.00273 ( 3) link_BETA1-4 : angle 0.91223 ( 9) link_NAG-ASN : bond 0.00276 ( 15) link_NAG-ASN : angle 2.08096 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5284.54 seconds wall clock time: 91 minutes 0.50 seconds (5460.50 seconds total)