Starting phenix.real_space_refine on Fri Sep 19 13:15:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jgh_61464/09_2025/9jgh_61464.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jgh_61464/09_2025/9jgh_61464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jgh_61464/09_2025/9jgh_61464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jgh_61464/09_2025/9jgh_61464.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jgh_61464/09_2025/9jgh_61464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jgh_61464/09_2025/9jgh_61464.map" } resolution = 3.7 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= 0.008 sd= 0.045 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 58 5.16 5 C 16291 2.51 5 N 4117 2.21 5 O 5155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25621 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1158 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 3 Chain: "B" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1249 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 4, 'TRANS': 152} Chain breaks: 2 Chain: "C" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1417 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain breaks: 1 Chain: "D" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1651 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain breaks: 3 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1748 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 1 Chain: "F" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "G" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1843 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "H" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "I" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1599 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 2 Chain: "J" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "K" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1806 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Chain: "L" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "M" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1814 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Chain: "N" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1906 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "O" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1806 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 6.78, per 1000 atoms: 0.26 Number of scatterers: 25621 At special positions: 0 Unit cell: (144.42, 127.82, 153.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 5155 8.00 N 4117 7.00 C 16291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6172 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 39 sheets defined 2.8% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 69 through 75 Processing helix chain 'C' and resid 69 through 77 removed outlier: 4.024A pdb=" N LEU C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.657A pdb=" N SER D 112 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP D 113 " --> pdb=" O PRO D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 109 through 113' Processing helix chain 'E' and resid 69 through 75 removed outlier: 4.423A pdb=" N LEU E 73 " --> pdb=" O ASP E 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'H' and resid 69 through 77 removed outlier: 3.591A pdb=" N LEU H 73 " --> pdb=" O ASP H 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 77 Processing helix chain 'J' and resid 69 through 77 removed outlier: 4.162A pdb=" N THR J 76 " --> pdb=" O TRP J 72 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN J 77 " --> pdb=" O LEU J 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 77 removed outlier: 3.717A pdb=" N LEU K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR K 76 " --> pdb=" O TRP K 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 47 Processing helix chain 'L' and resid 69 through 75 Processing helix chain 'O' and resid 70 through 75 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 4.404A pdb=" N VAL A 173 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 193 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 234 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU C 160 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU A 236 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG C 158 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG C 159 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLU C 83 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 65 removed outlier: 3.844A pdb=" N PHE A 32 " --> pdb=" O MET C 206 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET C 206 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.790A pdb=" N GLU A 221 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 15 removed outlier: 7.114A pdb=" N VAL B 11 " --> pdb=" O THR B 24 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR B 24 " --> pdb=" O VAL B 11 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 21 through 26 current: chain 'B' and resid 58 through 64 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 64 current: chain 'B' and resid 191 through 200 Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA6, first strand: chain 'B' and resid 82 through 88 removed outlier: 4.825A pdb=" N GLY B 157 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS B 86 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS B 155 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 22 removed outlier: 3.558A pdb=" N VAL C 22 " --> pdb=" O PHE C 13 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 198 through 201 removed outlier: 3.621A pdb=" N VAL C 63 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE C 220 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 61 " --> pdb=" O PHE C 220 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA C 222 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE C 59 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE C 32 " --> pdb=" O MET D 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 179 through 180 removed outlier: 7.437A pdb=" N ALA C 179 " --> pdb=" O TYR C 188 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA C 237 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL C 234 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU D 160 " --> pdb=" O VAL C 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 12 through 15 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 22 current: chain 'D' and resid 50 through 61 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 50 through 61 current: chain 'D' and resid 189 through 200 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 220 through 222 current: chain 'E' and resid 124 through 126 Processing sheet with id=AB2, first strand: chain 'D' and resid 27 through 30 removed outlier: 7.594A pdb=" N LYS D 64 " --> pdb=" O GLN D 28 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 91 through 93 removed outlier: 4.087A pdb=" N ALA D 149 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 13 through 15 Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 39 removed outlier: 3.509A pdb=" N THR E 62 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER E 37 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 56 " --> pdb=" O SER E 37 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS E 54 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE E 59 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA E 222 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 61 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE E 220 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU E 217 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU E 203 " --> pdb=" O GLU E 217 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LYS E 219 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER E 201 " --> pdb=" O LYS E 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 103 through 104 Processing sheet with id=AB7, first strand: chain 'E' and resid 175 through 176 removed outlier: 3.544A pdb=" N GLN E 194 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL E 233 " --> pdb=" O GLN E 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 15 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 21 through 22 current: chain 'F' and resid 190 through 200 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 220 through 222 current: chain 'J' and resid 125 through 126 Processing sheet with id=AB9, first strand: chain 'F' and resid 217 through 218 removed outlier: 3.555A pdb=" N VAL F 63 " --> pdb=" O ILE F 218 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE F 32 " --> pdb=" O MET J 206 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET J 206 " --> pdb=" O PHE F 32 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 82 through 89 removed outlier: 5.642A pdb=" N GLU F 83 " --> pdb=" O ARG F 159 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG F 159 " --> pdb=" O GLU F 83 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 153 through 163 current: chain 'H' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 63 current: chain 'H' and resid 149 through 162 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 149 through 162 current: chain 'H' and resid 189 through 208 removed outlier: 5.801A pdb=" N LYS H 219 " --> pdb=" O SER H 201 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 218 through 222 current: chain 'N' and resid 20 through 25 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 20 through 25 current: chain 'N' and resid 55 through 64 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 55 through 64 current: chain 'N' and resid 187 through 199 Processing sheet with id=AC2, first strand: chain 'F' and resid 92 through 97 removed outlier: 5.016A pdb=" N HIS F 94 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA F 149 " --> pdb=" O HIS F 94 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR F 148 " --> pdb=" O TYR F 117 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL F 114 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE F 126 " --> pdb=" O VAL F 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 103 through 104 Processing sheet with id=AC4, first strand: chain 'G' and resid 29 through 34 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 59 through 64 current: chain 'G' and resid 187 through 201 removed outlier: 4.331A pdb=" N LYS G 219 " --> pdb=" O SER G 201 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 217 through 222 current: chain 'K' and resid 158 through 160 Processing sheet with id=AC5, first strand: chain 'G' and resid 81 through 97 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 81 through 97 current: chain 'G' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 123 through 126 current: chain 'I' and resid 22 through 24 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 22 through 24 current: chain 'I' and resid 186 through 200 Processing sheet with id=AC6, first strand: chain 'I' and resid 27 through 32 removed outlier: 6.522A pdb=" N LYS I 64 " --> pdb=" O GLN I 28 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA I 30 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR I 62 " --> pdb=" O ALA I 30 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 85 through 86 removed outlier: 3.686A pdb=" N THR I 85 " --> pdb=" O GLY I 157 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL I 156 " --> pdb=" O SER O 238 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER O 238 " --> pdb=" O VAL I 156 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE O 195 " --> pdb=" O VAL O 173 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL O 173 " --> pdb=" O PHE O 195 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 89 through 91 removed outlier: 3.714A pdb=" N ILE I 153 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP I 91 " --> pdb=" O TYR I 151 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR I 151 " --> pdb=" O ASP I 91 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 206 through 208 removed outlier: 3.829A pdb=" N MET I 206 " --> pdb=" O PHE O 32 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU I 208 " --> pdb=" O ALA O 30 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA O 30 " --> pdb=" O LEU I 208 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR O 62 " --> pdb=" O SER O 31 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU O 61 " --> pdb=" O PHE O 220 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE O 220 " --> pdb=" O LEU O 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 15 removed outlier: 3.559A pdb=" N ALA J 25 " --> pdb=" O VAL J 11 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 25 through 26 current: chain 'J' and resid 189 through 194 removed outlier: 3.615A pdb=" N ASP J 190 " --> pdb=" O ALA J 237 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA J 237 " --> pdb=" O ASP J 190 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 232 through 238 current: chain 'L' and resid 123 through 127 Processing sheet with id=AD2, first strand: chain 'J' and resid 29 through 37 removed outlier: 3.502A pdb=" N ALA J 35 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU J 56 " --> pdb=" O SER J 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 55 through 64 current: chain 'J' and resid 217 through 222 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 217 through 222 current: chain 'L' and resid 49 through 64 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 49 through 64 current: chain 'L' and resid 187 through 209 removed outlier: 4.221A pdb=" N LYS L 219 " --> pdb=" O SER L 201 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU L 203 " --> pdb=" O GLU L 217 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU L 217 " --> pdb=" O GLU L 203 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 217 through 222 current: chain 'N' and resid 124 through 126 Processing sheet with id=AD3, first strand: chain 'J' and resid 103 through 105 Processing sheet with id=AD4, first strand: chain 'K' and resid 21 through 22 removed outlier: 3.709A pdb=" N PHE K 13 " --> pdb=" O VAL K 22 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR K 12 " --> pdb=" O GLU K 174 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU K 174 " --> pdb=" O TYR K 12 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR K 171 " --> pdb=" O ASN K 197 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN K 197 " --> pdb=" O TYR K 171 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL K 63 " --> pdb=" O ILE K 218 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE K 59 " --> pdb=" O ALA K 222 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE K 32 " --> pdb=" O MET M 206 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET M 206 " --> pdb=" O PHE K 32 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN K 34 " --> pdb=" O PHE M 204 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE M 204 " --> pdb=" O GLN K 34 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 87 through 97 removed outlier: 4.410A pdb=" N GLY K 95 " --> pdb=" O LEU K 147 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU K 147 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR K 115 " --> pdb=" O VAL K 150 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 103 through 105 Processing sheet with id=AD7, first strand: chain 'K' and resid 177 through 180 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 233 through 238 current: chain 'M' and resid 123 through 126 Processing sheet with id=AD8, first strand: chain 'L' and resid 103 through 105 Processing sheet with id=AD9, first strand: chain 'M' and resid 12 through 15 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 12 through 15 current: chain 'M' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 59 through 65 current: chain 'M' and resid 187 through 200 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 217 through 222 current: chain 'O' and resid 123 through 126 Processing sheet with id=AE1, first strand: chain 'M' and resid 103 through 104 Processing sheet with id=AE2, first strand: chain 'N' and resid 103 through 105 Processing sheet with id=AE3, first strand: chain 'O' and resid 103 through 105 262 hydrogen bonds defined for protein. 699 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: 4.51 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8314 1.34 - 1.46: 5728 1.46 - 1.58: 11875 1.58 - 1.70: 0 1.70 - 1.82: 116 Bond restraints: 26033 Sorted by residual: bond pdb=" N ASN I 65 " pdb=" CA ASN I 65 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.30e-02 5.92e+03 8.14e+00 bond pdb=" N ILE I 81 " pdb=" CA ILE I 81 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.87e+00 bond pdb=" N GLU I 79 " pdb=" CA GLU I 79 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.18e-02 7.18e+03 6.01e+00 bond pdb=" N GLN I 77 " pdb=" CA GLN I 77 " ideal model delta sigma weight residual 1.454 1.482 -0.029 1.17e-02 7.31e+03 5.96e+00 bond pdb=" N PHE I 68 " pdb=" CA PHE I 68 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.33e-02 5.65e+03 5.75e+00 ... (remaining 26028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 34634 2.38 - 4.76: 413 4.76 - 7.14: 50 7.14 - 9.53: 27 9.53 - 11.91: 6 Bond angle restraints: 35130 Sorted by residual: angle pdb=" CA ALA E 179 " pdb=" C ALA E 179 " pdb=" N TYR E 180 " ideal model delta sigma weight residual 116.84 127.93 -11.09 1.71e+00 3.42e-01 4.21e+01 angle pdb=" CA ALA E 179 " pdb=" C ALA E 179 " pdb=" O ALA E 179 " ideal model delta sigma weight residual 120.51 113.32 7.19 1.43e+00 4.89e-01 2.53e+01 angle pdb=" N LEU I 70 " pdb=" CA LEU I 70 " pdb=" C LEU I 70 " ideal model delta sigma weight residual 113.97 107.85 6.12 1.28e+00 6.10e-01 2.28e+01 angle pdb=" C LYS H 146 " pdb=" N LEU H 147 " pdb=" CA LEU H 147 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C ILE G 52 " pdb=" N LEU G 53 " pdb=" CA LEU G 53 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 ... (remaining 35125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 13401 17.81 - 35.62: 1803 35.62 - 53.43: 516 53.43 - 71.24: 120 71.24 - 89.06: 44 Dihedral angle restraints: 15884 sinusoidal: 6369 harmonic: 9515 Sorted by residual: dihedral pdb=" CA TYR E 180 " pdb=" C TYR E 180 " pdb=" N ASN E 181 " pdb=" CA ASN E 181 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA TRP O 72 " pdb=" C TRP O 72 " pdb=" N LEU O 73 " pdb=" CA LEU O 73 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ILE E 178 " pdb=" C ILE E 178 " pdb=" N ALA E 179 " pdb=" CA ALA E 179 " ideal model delta harmonic sigma weight residual -180.00 -157.51 -22.49 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 15881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3282 0.055 - 0.110: 624 0.110 - 0.165: 98 0.165 - 0.221: 2 0.221 - 0.276: 2 Chirality restraints: 4008 Sorted by residual: chirality pdb=" CB ILE D 45 " pdb=" CA ILE D 45 " pdb=" CG1 ILE D 45 " pdb=" CG2 ILE D 45 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB ILE B 45 " pdb=" CA ILE B 45 " pdb=" CG1 ILE B 45 " pdb=" CG2 ILE B 45 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB ILE I 59 " pdb=" CA ILE I 59 " pdb=" CG1 ILE I 59 " pdb=" CG2 ILE I 59 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.88e-01 ... (remaining 4005 not shown) Planarity restraints: 4506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 64 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LYS I 64 " 0.062 2.00e-02 2.50e+03 pdb=" O LYS I 64 " -0.023 2.00e-02 2.50e+03 pdb=" N ASN I 65 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 229 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" CG ASP F 229 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP F 229 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 229 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 72 " 0.018 2.00e-02 2.50e+03 1.34e-02 4.46e+00 pdb=" CG TRP H 72 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP H 72 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP H 72 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 72 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 72 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 72 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 72 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 72 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 72 " 0.007 2.00e-02 2.50e+03 ... (remaining 4503 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1313 2.71 - 3.25: 25792 3.25 - 3.80: 42884 3.80 - 4.35: 50712 4.35 - 4.90: 83275 Nonbonded interactions: 203976 Sorted by model distance: nonbonded pdb=" OD2 ASP L 190 " pdb=" OH TYR L 192 " model vdw 2.158 3.040 nonbonded pdb=" N GLN C 6 " pdb=" O ASN D 210 " model vdw 2.158 3.120 nonbonded pdb=" OH TYR B 51 " pdb=" O ASN H 181 " model vdw 2.165 3.040 nonbonded pdb=" OG1 THR J 3 " pdb=" O TYR J 180 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR K 80 " pdb=" OE1 GLN K 82 " model vdw 2.207 3.040 ... (remaining 203971 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 178 or resid 190 through 237)) selection = (chain 'B' and (resid 9 through 16 or resid 22 through 77 or resid 155 through 2 \ 37)) } ncs_group { reference = (chain 'C' and (resid 1 through 40 or resid 58 through 183 or resid 187 through \ 241)) selection = (chain 'D' and (resid 1 through 40 or resid 58 through 89 or resid 153 through 2 \ 41)) selection = (chain 'I' and (resid 1 through 89 or resid 153 through 183 or resid 187 through \ 241)) } ncs_group { reference = (chain 'E' and (resid 12 through 39 or resid 53 through 238)) selection = (chain 'F' and (resid 12 through 39 or resid 53 through 181 or resid 188 through \ 238)) selection = (chain 'G' and (resid 12 through 39 or resid 53 through 181 or resid 188 through \ 238)) selection = (chain 'H' and (resid 12 through 39 or resid 53 through 181 or resid 188 through \ 238)) selection = (chain 'J' and (resid 12 through 39 or resid 53 through 181 or resid 188 through \ 238)) selection = (chain 'K' and (resid 12 through 181 or resid 188 through 238)) selection = (chain 'L' and (resid 12 through 39 or resid 53 through 181 or resid 188 through \ 238)) selection = (chain 'M' and (resid 12 through 39 or resid 53 through 181 or resid 188 through \ 238)) selection = (chain 'N' and (resid 12 through 39 or resid 53 through 181 or resid 188 through \ 238)) selection = (chain 'O' and (resid 12 through 181 or resid 188 through 238)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.090 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.002 0.037 26033 Z= 0.135 Angle : 0.675 11.907 35130 Z= 0.351 Chirality : 0.045 0.276 4008 Planarity : 0.003 0.045 4506 Dihedral : 18.387 89.056 9712 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.18 % Favored : 90.51 % Rotamer: Outliers : 0.07 % Allowed : 34.02 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.14), residues: 3171 helix: -3.00 (0.47), residues: 70 sheet: 0.20 (0.16), residues: 1135 loop : -2.25 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 176 TYR 0.014 0.001 TYR A 51 PHE 0.035 0.001 PHE J 23 TRP 0.035 0.002 TRP H 72 HIS 0.001 0.000 HIS K 94 Details of bonding type rmsd covalent geometry : bond 0.00248 (26033) covalent geometry : angle 0.67524 (35130) hydrogen bonds : bond 0.30170 ( 262) hydrogen bonds : angle 12.18260 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.7435 (t0) cc_final: 0.7145 (t0) REVERT: A 12 TYR cc_start: 0.7639 (m-80) cc_final: 0.7260 (m-10) REVERT: A 176 ARG cc_start: 0.7032 (ttp80) cc_final: 0.6643 (tmm160) REVERT: F 71 GLU cc_start: 0.7632 (mp0) cc_final: 0.7421 (mp0) REVERT: M 231 MET cc_start: 0.7565 (mtm) cc_final: 0.7359 (mtp) REVERT: N 54 LYS cc_start: 0.7936 (pttt) cc_final: 0.7573 (tptt) outliers start: 2 outliers final: 0 residues processed: 221 average time/residue: 0.1699 time to fit residues: 60.9168 Evaluate side-chains 190 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 0.0970 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 40.0000 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN F 28 GLN ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 ASN ** N 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 197 ASN O 6 GLN O 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.056088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.042573 restraints weight = 208887.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.043659 restraints weight = 134919.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.044393 restraints weight = 99784.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.044910 restraints weight = 80642.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.045263 restraints weight = 69308.498| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26033 Z= 0.147 Angle : 0.598 9.584 35130 Z= 0.306 Chirality : 0.044 0.283 4008 Planarity : 0.003 0.044 4506 Dihedral : 4.495 26.416 3452 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.34 % Favored : 89.34 % Rotamer: Outliers : 4.06 % Allowed : 31.28 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.15), residues: 3171 helix: -2.30 (0.52), residues: 72 sheet: -0.20 (0.15), residues: 1270 loop : -2.17 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 42 TYR 0.014 0.001 TYR D 175 PHE 0.022 0.001 PHE J 23 TRP 0.019 0.002 TRP L 72 HIS 0.001 0.000 HIS H 94 Details of bonding type rmsd covalent geometry : bond 0.00322 (26033) covalent geometry : angle 0.59846 (35130) hydrogen bonds : bond 0.04572 ( 262) hydrogen bonds : angle 8.31469 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 193 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7829 (tpt-90) cc_final: 0.7397 (tpt170) REVERT: A 192 TYR cc_start: 0.8838 (m-10) cc_final: 0.8028 (m-10) REVERT: A 208 LEU cc_start: 0.8646 (tp) cc_final: 0.8222 (pp) REVERT: C 47 ASN cc_start: 0.8684 (t0) cc_final: 0.8439 (t0) REVERT: C 203 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7814 (mm-30) REVERT: D 198 VAL cc_start: 0.4781 (OUTLIER) cc_final: 0.3918 (m) REVERT: D 220 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7329 (t80) REVERT: D 233 VAL cc_start: 0.6691 (OUTLIER) cc_final: 0.6207 (t) REVERT: F 71 GLU cc_start: 0.7871 (mp0) cc_final: 0.7622 (mp0) REVERT: G 26 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8251 (tp30) REVERT: H 1 MET cc_start: 0.6789 (tpp) cc_final: 0.6139 (tpp) REVERT: H 75 MET cc_start: 0.9321 (tpp) cc_final: 0.9064 (tpp) REVERT: H 206 MET cc_start: 0.8671 (pmm) cc_final: 0.8327 (pmm) REVERT: I 231 MET cc_start: 0.9063 (pmm) cc_final: 0.8757 (pmm) REVERT: J 31 SER cc_start: 0.9648 (OUTLIER) cc_final: 0.9298 (m) REVERT: J 204 PHE cc_start: 0.7754 (m-80) cc_final: 0.7483 (m-10) REVERT: K 113 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8817 (t0) REVERT: L 75 MET cc_start: 0.9274 (tpp) cc_final: 0.9024 (tpp) REVERT: L 158 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8839 (ptp-170) REVERT: L 241 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: M 212 ASN cc_start: 0.9285 (t0) cc_final: 0.9005 (t0) REVERT: N 209 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: N 231 MET cc_start: 0.9577 (OUTLIER) cc_final: 0.8844 (mmp) REVERT: O 170 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6926 (ttp80) REVERT: O 171 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7921 (t80) REVERT: O 176 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8397 (ttp80) outliers start: 113 outliers final: 42 residues processed: 293 average time/residue: 0.1750 time to fit residues: 80.9516 Evaluate side-chains 230 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 174 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 180 TYR Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain M residue 56 GLU Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 209 GLU Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 171 TYR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 234 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 99 optimal weight: 20.0000 chunk 269 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 309 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 161 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN ** N 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.053623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.040467 restraints weight = 218938.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.041543 restraints weight = 138724.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.042262 restraints weight = 101388.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.042769 restraints weight = 81511.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.043095 restraints weight = 69621.744| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26033 Z= 0.198 Angle : 0.630 8.935 35130 Z= 0.325 Chirality : 0.045 0.287 4008 Planarity : 0.004 0.052 4506 Dihedral : 4.921 25.727 3452 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.91 % Favored : 88.77 % Rotamer: Outliers : 5.61 % Allowed : 30.35 % Favored : 64.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.14), residues: 3171 helix: -2.05 (0.55), residues: 66 sheet: -0.48 (0.15), residues: 1240 loop : -2.16 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 42 TYR 0.023 0.001 TYR A 51 PHE 0.020 0.002 PHE J 23 TRP 0.038 0.002 TRP H 72 HIS 0.002 0.001 HIS O 94 Details of bonding type rmsd covalent geometry : bond 0.00423 (26033) covalent geometry : angle 0.63028 (35130) hydrogen bonds : bond 0.04268 ( 262) hydrogen bonds : angle 7.85936 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 174 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7633 (m-40) REVERT: A 176 ARG cc_start: 0.8498 (tpt90) cc_final: 0.8260 (tpm170) REVERT: A 208 LEU cc_start: 0.8734 (tp) cc_final: 0.8295 (pp) REVERT: C 47 ASN cc_start: 0.8967 (t0) cc_final: 0.8523 (t0) REVERT: C 203 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8403 (mp0) REVERT: D 53 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5638 (mp) REVERT: D 175 TYR cc_start: 0.8805 (m-80) cc_final: 0.8554 (m-10) REVERT: D 198 VAL cc_start: 0.5037 (OUTLIER) cc_final: 0.4264 (m) REVERT: D 220 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7478 (t80) REVERT: F 71 GLU cc_start: 0.8001 (mp0) cc_final: 0.7650 (mp0) REVERT: F 231 MET cc_start: 0.8917 (ppp) cc_final: 0.8203 (ppp) REVERT: G 26 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8452 (tp30) REVERT: G 34 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8958 (pp30) REVERT: G 171 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: G 176 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8639 (tmm-80) REVERT: H 1 MET cc_start: 0.7478 (tpp) cc_final: 0.6614 (tpp) REVERT: H 60 ASN cc_start: 0.9650 (m-40) cc_final: 0.9004 (p0) REVERT: H 64 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8485 (mmmm) REVERT: H 75 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9120 (tpp) REVERT: H 187 VAL cc_start: 0.9610 (OUTLIER) cc_final: 0.9358 (t) REVERT: H 206 MET cc_start: 0.8851 (pmm) cc_final: 0.8424 (pmm) REVERT: J 1 MET cc_start: 0.8080 (tmm) cc_final: 0.7849 (tmm) REVERT: K 88 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8846 (mmtm) REVERT: K 113 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8796 (t0) REVERT: K 146 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8632 (ttpp) REVERT: L 75 MET cc_start: 0.9219 (tpp) cc_final: 0.8968 (tpp) REVERT: L 158 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8762 (ptm160) REVERT: L 241 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: M 212 ASN cc_start: 0.9409 (t0) cc_final: 0.9042 (t0) REVERT: M 231 MET cc_start: 0.9026 (mtp) cc_final: 0.8504 (mtp) REVERT: N 231 MET cc_start: 0.9572 (OUTLIER) cc_final: 0.9048 (mmp) outliers start: 156 outliers final: 81 residues processed: 314 average time/residue: 0.1660 time to fit residues: 83.4471 Evaluate side-chains 255 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 157 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain M residue 56 GLU Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain N residue 120 LYS Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 144 LYS Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 234 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 4 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 58 optimal weight: 50.0000 chunk 11 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 26 optimal weight: 50.0000 chunk 292 optimal weight: 8.9990 chunk 271 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.053979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.040855 restraints weight = 217144.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.041927 restraints weight = 136817.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.042657 restraints weight = 99825.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.043167 restraints weight = 79984.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.043523 restraints weight = 68286.106| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26033 Z= 0.143 Angle : 0.596 9.394 35130 Z= 0.303 Chirality : 0.044 0.278 4008 Planarity : 0.003 0.051 4506 Dihedral : 4.787 21.520 3452 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.53 % Favored : 89.15 % Rotamer: Outliers : 5.11 % Allowed : 30.89 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.14), residues: 3171 helix: -1.93 (0.58), residues: 64 sheet: -0.48 (0.15), residues: 1235 loop : -2.11 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 159 TYR 0.024 0.001 TYR A 51 PHE 0.025 0.001 PHE J 23 TRP 0.048 0.003 TRP H 72 HIS 0.001 0.000 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00311 (26033) covalent geometry : angle 0.59639 (35130) hydrogen bonds : bond 0.03658 ( 262) hydrogen bonds : angle 7.56194 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 176 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7006 (pp) REVERT: A 208 LEU cc_start: 0.8909 (tp) cc_final: 0.8505 (pp) REVERT: B 206 MET cc_start: 0.6736 (pmm) cc_final: 0.6398 (pmm) REVERT: C 47 ASN cc_start: 0.9024 (t0) cc_final: 0.8551 (t0) REVERT: C 203 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: C 206 MET cc_start: 0.9370 (pmm) cc_final: 0.8825 (pmm) REVERT: D 175 TYR cc_start: 0.8892 (m-80) cc_final: 0.8690 (m-80) REVERT: D 198 VAL cc_start: 0.5453 (OUTLIER) cc_final: 0.4646 (m) REVERT: D 220 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7475 (t80) REVERT: F 28 GLN cc_start: 0.8733 (tm-30) cc_final: 0.7983 (tp40) REVERT: F 71 GLU cc_start: 0.8036 (mp0) cc_final: 0.7699 (mp0) REVERT: F 231 MET cc_start: 0.8952 (ppp) cc_final: 0.8334 (ppp) REVERT: G 26 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8417 (tp30) REVERT: G 102 ASN cc_start: 0.6786 (OUTLIER) cc_final: 0.6507 (t0) REVERT: G 171 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: G 176 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8570 (tmm-80) REVERT: H 1 MET cc_start: 0.7692 (tpp) cc_final: 0.6738 (tpp) REVERT: H 60 ASN cc_start: 0.9638 (m-40) cc_final: 0.8985 (p0) REVERT: H 75 MET cc_start: 0.9331 (tpp) cc_final: 0.9092 (tpp) REVERT: H 206 MET cc_start: 0.8896 (pmm) cc_final: 0.8600 (pmm) REVERT: I 214 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8430 (mm) REVERT: J 1 MET cc_start: 0.8165 (tmm) cc_final: 0.7957 (tmm) REVERT: J 40 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7427 (mmmt) REVERT: K 88 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8842 (mmtm) REVERT: K 113 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8741 (t0) REVERT: K 146 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8672 (ttpp) REVERT: L 75 MET cc_start: 0.9251 (tpp) cc_final: 0.8969 (tpp) REVERT: L 158 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8797 (ptm160) REVERT: L 241 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: M 56 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6484 (pm20) REVERT: M 212 ASN cc_start: 0.9444 (t0) cc_final: 0.9047 (t0) REVERT: N 120 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9149 (pttp) REVERT: N 231 MET cc_start: 0.9545 (OUTLIER) cc_final: 0.8859 (mmp) REVERT: O 170 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7332 (ttp80) REVERT: O 176 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8262 (ttp80) outliers start: 142 outliers final: 83 residues processed: 304 average time/residue: 0.1737 time to fit residues: 83.9104 Evaluate side-chains 271 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 168 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 56 GLU Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 120 LYS Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 65 ASN Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 234 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 316 optimal weight: 50.0000 chunk 107 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 204 optimal weight: 4.9990 chunk 16 optimal weight: 50.0000 chunk 261 optimal weight: 30.0000 chunk 244 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 23 optimal weight: 50.0000 overall best weight: 10.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN C 34 GLN D 60 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.050993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.038297 restraints weight = 222832.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.039302 restraints weight = 139660.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.039990 restraints weight = 101572.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.040455 restraints weight = 81341.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.040772 restraints weight = 69688.079| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 26033 Z= 0.271 Angle : 0.704 8.776 35130 Z= 0.368 Chirality : 0.046 0.269 4008 Planarity : 0.004 0.054 4506 Dihedral : 5.610 29.632 3452 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.20 % Favored : 87.42 % Rotamer: Outliers : 6.69 % Allowed : 30.53 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.14), residues: 3171 helix: -2.37 (0.51), residues: 77 sheet: -0.78 (0.15), residues: 1183 loop : -2.31 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 92 TYR 0.041 0.002 TYR A 51 PHE 0.027 0.002 PHE N 23 TRP 0.038 0.003 TRP O 72 HIS 0.003 0.001 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00576 (26033) covalent geometry : angle 0.70407 (35130) hydrogen bonds : bond 0.04180 ( 262) hydrogen bonds : angle 7.91580 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 168 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7492 (pp) REVERT: A 208 LEU cc_start: 0.8869 (tp) cc_final: 0.8489 (pp) REVERT: B 50 LEU cc_start: 0.8976 (mt) cc_final: 0.8639 (mt) REVERT: B 206 MET cc_start: 0.7060 (pmm) cc_final: 0.6836 (pmm) REVERT: C 47 ASN cc_start: 0.9030 (t0) cc_final: 0.8613 (t0) REVERT: C 203 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8509 (mm-30) REVERT: C 206 MET cc_start: 0.9402 (pmm) cc_final: 0.8928 (pmm) REVERT: D 81 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7980 (tp) REVERT: D 151 TYR cc_start: 0.9201 (OUTLIER) cc_final: 0.8899 (p90) REVERT: D 175 TYR cc_start: 0.9215 (m-80) cc_final: 0.8902 (m-80) REVERT: D 210 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7937 (m-40) REVERT: F 1 MET cc_start: 0.8716 (ppp) cc_final: 0.8411 (tmm) REVERT: F 23 PHE cc_start: 0.6543 (t80) cc_final: 0.5319 (t80) REVERT: F 28 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8093 (tp40) REVERT: F 231 MET cc_start: 0.8943 (ppp) cc_final: 0.8193 (ppp) REVERT: G 171 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: G 176 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8722 (tmm-80) REVERT: H 1 MET cc_start: 0.8042 (tpp) cc_final: 0.7000 (tpp) REVERT: H 60 ASN cc_start: 0.9685 (m-40) cc_final: 0.9120 (p0) REVERT: H 206 MET cc_start: 0.8990 (pmm) cc_final: 0.8534 (pmm) REVERT: H 219 LYS cc_start: 0.9315 (mtpp) cc_final: 0.9007 (mmmt) REVERT: J 1 MET cc_start: 0.8273 (tmm) cc_final: 0.7829 (tmm) REVERT: K 88 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8947 (mmtm) REVERT: K 146 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8823 (tmtt) REVERT: L 75 MET cc_start: 0.9182 (tpp) cc_final: 0.8922 (tpp) REVERT: L 241 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8798 (mp0) REVERT: M 206 MET cc_start: 0.8427 (pmm) cc_final: 0.7133 (pmm) REVERT: M 212 ASN cc_start: 0.9525 (t0) cc_final: 0.9127 (t0) REVERT: M 231 MET cc_start: 0.9253 (mtp) cc_final: 0.8639 (mmm) REVERT: N 231 MET cc_start: 0.9632 (OUTLIER) cc_final: 0.9067 (mmp) REVERT: O 176 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8270 (ttp80) REVERT: O 201 SER cc_start: 0.5162 (OUTLIER) cc_final: 0.4685 (t) outliers start: 186 outliers final: 111 residues processed: 334 average time/residue: 0.1718 time to fit residues: 91.0238 Evaluate side-chains 285 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 161 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 217 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 227 ASP Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 120 LYS Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 65 ASN Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 234 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 100 optimal weight: 30.0000 chunk 220 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 283 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 197 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 250 optimal weight: 20.0000 chunk 56 optimal weight: 50.0000 chunk 134 optimal weight: 10.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 77 GLN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.051173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.038608 restraints weight = 229382.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.039633 restraints weight = 141861.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.040326 restraints weight = 102596.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.040775 restraints weight = 82000.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.041089 restraints weight = 70440.556| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26033 Z= 0.232 Angle : 0.669 8.333 35130 Z= 0.346 Chirality : 0.045 0.271 4008 Planarity : 0.004 0.064 4506 Dihedral : 5.570 29.211 3452 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.29 % Favored : 88.36 % Rotamer: Outliers : 5.93 % Allowed : 31.54 % Favored : 62.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.14), residues: 3171 helix: -2.57 (0.46), residues: 84 sheet: -0.84 (0.15), residues: 1238 loop : -2.33 (0.13), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 159 TYR 0.032 0.002 TYR A 51 PHE 0.021 0.002 PHE F 195 TRP 0.072 0.004 TRP H 72 HIS 0.002 0.001 HIS G 94 Details of bonding type rmsd covalent geometry : bond 0.00496 (26033) covalent geometry : angle 0.66909 (35130) hydrogen bonds : bond 0.03829 ( 262) hydrogen bonds : angle 7.73132 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 171 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LEU cc_start: 0.9048 (tp) cc_final: 0.8734 (pp) REVERT: A 229 ASP cc_start: 0.9767 (p0) cc_final: 0.9559 (p0) REVERT: B 50 LEU cc_start: 0.9161 (mt) cc_final: 0.8821 (mt) REVERT: B 206 MET cc_start: 0.7027 (pmm) cc_final: 0.6803 (pmm) REVERT: C 47 ASN cc_start: 0.9132 (t0) cc_final: 0.8742 (t0) REVERT: C 203 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8608 (mm-30) REVERT: C 206 MET cc_start: 0.9451 (pmm) cc_final: 0.9058 (pmm) REVERT: D 151 TYR cc_start: 0.9221 (OUTLIER) cc_final: 0.8928 (p90) REVERT: D 175 TYR cc_start: 0.9314 (m-80) cc_final: 0.8946 (m-80) REVERT: D 220 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8123 (t80) REVERT: F 1 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8335 (tmm) REVERT: F 2 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8680 (tptp) REVERT: F 23 PHE cc_start: 0.6356 (t80) cc_final: 0.5312 (t80) REVERT: F 28 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8180 (tp40) REVERT: F 72 TRP cc_start: 0.7832 (m100) cc_final: 0.7522 (m100) REVERT: F 231 MET cc_start: 0.8893 (ppp) cc_final: 0.8108 (ppp) REVERT: G 26 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8596 (tp30) REVERT: G 171 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: G 176 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8760 (tmm-80) REVERT: H 1 MET cc_start: 0.8159 (tpp) cc_final: 0.7222 (tpp) REVERT: H 23 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: H 206 MET cc_start: 0.9045 (pmm) cc_final: 0.8618 (pmm) REVERT: H 219 LYS cc_start: 0.9328 (mtpp) cc_final: 0.9015 (mmmt) REVERT: J 1 MET cc_start: 0.8395 (tmm) cc_final: 0.7933 (tmm) REVERT: K 88 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8977 (mmtm) REVERT: K 113 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8782 (t0) REVERT: K 146 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8794 (ttpp) REVERT: L 1 MET cc_start: 0.8464 (ptm) cc_final: 0.8015 (ptm) REVERT: L 241 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8745 (mp0) REVERT: M 212 ASN cc_start: 0.9564 (t0) cc_final: 0.9188 (t0) REVERT: N 41 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9112 (pp) REVERT: N 231 MET cc_start: 0.9608 (OUTLIER) cc_final: 0.8726 (mmp) REVERT: O 201 SER cc_start: 0.5178 (OUTLIER) cc_final: 0.4736 (t) outliers start: 165 outliers final: 111 residues processed: 318 average time/residue: 0.1658 time to fit residues: 84.4698 Evaluate side-chains 288 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 161 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain G residue 239 ARG Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain H residue 23 PHE Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 163 LYS Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 75 MET Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 217 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 227 ASP Chi-restraints excluded: chain L residue 229 ASP Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 120 LYS Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 234 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 181 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 277 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 chunk 159 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 chunk 98 optimal weight: 40.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.052701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.040214 restraints weight = 215966.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.041231 restraints weight = 132968.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.041957 restraints weight = 96188.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.042453 restraints weight = 76406.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.042818 restraints weight = 64765.864| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26033 Z= 0.125 Angle : 0.632 13.066 35130 Z= 0.320 Chirality : 0.045 0.265 4008 Planarity : 0.003 0.051 4506 Dihedral : 5.107 26.988 3452 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.88 % Favored : 88.77 % Rotamer: Outliers : 4.96 % Allowed : 32.69 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.14), residues: 3171 helix: -1.79 (0.54), residues: 71 sheet: -0.70 (0.15), residues: 1270 loop : -2.27 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 158 TYR 0.028 0.001 TYR A 51 PHE 0.023 0.001 PHE J 23 TRP 0.043 0.003 TRP H 72 HIS 0.001 0.000 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00275 (26033) covalent geometry : angle 0.63197 (35130) hydrogen bonds : bond 0.03296 ( 262) hydrogen bonds : angle 7.27122 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 185 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8434 (m-10) cc_final: 0.8201 (m-10) REVERT: A 168 SER cc_start: 0.8574 (OUTLIER) cc_final: 0.8124 (t) REVERT: A 208 LEU cc_start: 0.9044 (tp) cc_final: 0.8753 (pp) REVERT: A 229 ASP cc_start: 0.9744 (p0) cc_final: 0.9508 (p0) REVERT: B 50 LEU cc_start: 0.9110 (mt) cc_final: 0.8524 (mp) REVERT: B 206 MET cc_start: 0.7185 (pmm) cc_final: 0.6661 (pmm) REVERT: B 225 ASP cc_start: 0.9261 (p0) cc_final: 0.9046 (p0) REVERT: C 47 ASN cc_start: 0.9176 (t0) cc_final: 0.8805 (t0) REVERT: C 203 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8585 (mm-30) REVERT: C 206 MET cc_start: 0.9476 (pmm) cc_final: 0.9035 (pmm) REVERT: D 151 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8812 (p90) REVERT: D 175 TYR cc_start: 0.9293 (m-80) cc_final: 0.8926 (m-80) REVERT: D 220 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8142 (t80) REVERT: F 1 MET cc_start: 0.8683 (ppp) cc_final: 0.8296 (tmm) REVERT: F 23 PHE cc_start: 0.6265 (t80) cc_final: 0.4935 (t80) REVERT: F 28 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8091 (tm-30) REVERT: F 72 TRP cc_start: 0.7895 (m100) cc_final: 0.7617 (m100) REVERT: F 119 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9148 (mttp) REVERT: F 231 MET cc_start: 0.8974 (ppp) cc_final: 0.8159 (ppp) REVERT: G 26 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8644 (tp30) REVERT: G 34 GLN cc_start: 0.9409 (OUTLIER) cc_final: 0.9188 (pp30) REVERT: G 171 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: G 176 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8556 (tmm-80) REVERT: H 1 MET cc_start: 0.8255 (tpp) cc_final: 0.7529 (tpp) REVERT: H 23 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: H 60 ASN cc_start: 0.9645 (m-40) cc_final: 0.8950 (p0) REVERT: H 171 TYR cc_start: 0.9090 (m-80) cc_final: 0.8823 (m-80) REVERT: H 187 VAL cc_start: 0.9592 (OUTLIER) cc_final: 0.9335 (t) REVERT: H 206 MET cc_start: 0.9070 (pmm) cc_final: 0.8766 (pmm) REVERT: J 1 MET cc_start: 0.8410 (tmm) cc_final: 0.7911 (tmm) REVERT: K 88 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8994 (mmtm) REVERT: K 113 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8746 (t0) REVERT: K 146 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8898 (tmtt) REVERT: L 1 MET cc_start: 0.8267 (ptm) cc_final: 0.7845 (ptm) REVERT: L 50 LEU cc_start: 0.9037 (mt) cc_final: 0.8710 (mt) REVERT: L 64 LYS cc_start: 0.9220 (ttpp) cc_final: 0.8996 (ttpp) REVERT: L 241 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8792 (mp0) REVERT: M 212 ASN cc_start: 0.9511 (t0) cc_final: 0.9117 (t0) REVERT: M 231 MET cc_start: 0.9050 (mtp) cc_final: 0.8315 (mmm) REVERT: M 239 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7319 (tpm170) REVERT: N 21 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8570 (mp) REVERT: N 120 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9194 (pttp) REVERT: N 231 MET cc_start: 0.9520 (OUTLIER) cc_final: 0.8791 (mmp) REVERT: O 201 SER cc_start: 0.4829 (OUTLIER) cc_final: 0.4228 (t) outliers start: 138 outliers final: 91 residues processed: 306 average time/residue: 0.1691 time to fit residues: 82.1545 Evaluate side-chains 284 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 173 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 TYR Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 34 GLN Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain H residue 23 PHE Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 241 GLU Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 120 LYS Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 65 ASN Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 171 TYR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 208 LEU Chi-restraints excluded: chain O residue 234 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 269 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 230 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 chunk 112 optimal weight: 30.0000 chunk 160 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 297 optimal weight: 20.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 47 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.051519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.038857 restraints weight = 225076.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.039888 restraints weight = 139430.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.040584 restraints weight = 100693.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.041060 restraints weight = 80562.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041383 restraints weight = 69022.526| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26033 Z= 0.181 Angle : 0.659 14.935 35130 Z= 0.333 Chirality : 0.045 0.262 4008 Planarity : 0.004 0.062 4506 Dihedral : 5.254 26.797 3452 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.38 % Favored : 88.30 % Rotamer: Outliers : 5.29 % Allowed : 32.33 % Favored : 62.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.14), residues: 3171 helix: -1.95 (0.55), residues: 76 sheet: -0.76 (0.15), residues: 1262 loop : -2.23 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 42 TYR 0.032 0.001 TYR A 51 PHE 0.025 0.002 PHE J 23 TRP 0.037 0.003 TRP H 72 HIS 0.001 0.001 HIS O 94 Details of bonding type rmsd covalent geometry : bond 0.00392 (26033) covalent geometry : angle 0.65863 (35130) hydrogen bonds : bond 0.03400 ( 262) hydrogen bonds : angle 7.28507 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 175 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8470 (m-10) cc_final: 0.8212 (m-10) REVERT: A 168 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8159 (t) REVERT: A 208 LEU cc_start: 0.9072 (tp) cc_final: 0.8780 (pp) REVERT: A 229 ASP cc_start: 0.9707 (p0) cc_final: 0.9449 (p0) REVERT: B 23 PHE cc_start: 0.9053 (t80) cc_final: 0.8751 (t80) REVERT: B 50 LEU cc_start: 0.9115 (mt) cc_final: 0.8894 (mt) REVERT: B 225 ASP cc_start: 0.9219 (p0) cc_final: 0.9018 (p0) REVERT: C 47 ASN cc_start: 0.9162 (t0) cc_final: 0.8728 (t0) REVERT: C 203 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8555 (mm-30) REVERT: C 206 MET cc_start: 0.9446 (pmm) cc_final: 0.9060 (pmm) REVERT: D 151 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8901 (p90) REVERT: D 175 TYR cc_start: 0.9365 (m-80) cc_final: 0.8941 (m-80) REVERT: E 206 MET cc_start: 0.2877 (ttt) cc_final: 0.2677 (ttt) REVERT: F 1 MET cc_start: 0.8667 (ppp) cc_final: 0.8301 (tmm) REVERT: F 23 PHE cc_start: 0.6318 (t80) cc_final: 0.6006 (t80) REVERT: F 28 GLN cc_start: 0.8648 (tm-30) cc_final: 0.7974 (tp-100) REVERT: F 119 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9212 (mttp) REVERT: F 231 MET cc_start: 0.8894 (ppp) cc_final: 0.7651 (ppp) REVERT: G 26 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8614 (tp30) REVERT: G 90 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8592 (t80) REVERT: G 171 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: G 176 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8791 (tmm-80) REVERT: H 1 MET cc_start: 0.8375 (tpp) cc_final: 0.7530 (tpp) REVERT: H 23 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: H 206 MET cc_start: 0.9021 (pmm) cc_final: 0.8618 (pmm) REVERT: I 206 MET cc_start: 0.8161 (tmm) cc_final: 0.7898 (ppp) REVERT: J 1 MET cc_start: 0.8524 (tmm) cc_final: 0.8016 (tmm) REVERT: K 88 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8918 (mmtm) REVERT: K 113 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8728 (t0) REVERT: K 146 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8882 (tmtt) REVERT: L 1 MET cc_start: 0.8279 (ptm) cc_final: 0.7840 (ptm) REVERT: M 212 ASN cc_start: 0.9542 (t0) cc_final: 0.9149 (t0) REVERT: M 231 MET cc_start: 0.9140 (mtp) cc_final: 0.7980 (mmm) REVERT: M 239 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7358 (tpm170) REVERT: N 148 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8234 (t) REVERT: N 152 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.8799 (mp10) REVERT: N 231 MET cc_start: 0.9603 (OUTLIER) cc_final: 0.8855 (mmp) REVERT: O 166 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7571 (pptt) REVERT: O 201 SER cc_start: 0.5382 (OUTLIER) cc_final: 0.4821 (t) outliers start: 147 outliers final: 110 residues processed: 304 average time/residue: 0.1751 time to fit residues: 84.2224 Evaluate side-chains 299 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 171 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 12 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 TYR Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 90 PHE Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain H residue 23 PHE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 120 LYS Chi-restraints excluded: chain N residue 148 THR Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 65 ASN Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 166 LYS Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 204 PHE Chi-restraints excluded: chain O residue 208 LEU Chi-restraints excluded: chain O residue 234 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 104 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 311 optimal weight: 7.9990 chunk 278 optimal weight: 0.5980 chunk 3 optimal weight: 9.9990 chunk 147 optimal weight: 30.0000 chunk 134 optimal weight: 30.0000 chunk 264 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 47 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.052088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.039321 restraints weight = 219460.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.040367 restraints weight = 135449.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.041080 restraints weight = 97811.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.041569 restraints weight = 77982.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.041878 restraints weight = 66563.132| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26033 Z= 0.143 Angle : 0.652 14.423 35130 Z= 0.326 Chirality : 0.045 0.265 4008 Planarity : 0.003 0.076 4506 Dihedral : 5.138 25.695 3452 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.56 % Favored : 89.12 % Rotamer: Outliers : 4.82 % Allowed : 32.61 % Favored : 62.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.14), residues: 3171 helix: -1.77 (0.56), residues: 71 sheet: -0.71 (0.15), residues: 1250 loop : -2.23 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 42 TYR 0.028 0.001 TYR A 51 PHE 0.027 0.001 PHE J 204 TRP 0.033 0.002 TRP L 72 HIS 0.001 0.000 HIS F 94 Details of bonding type rmsd covalent geometry : bond 0.00318 (26033) covalent geometry : angle 0.65224 (35130) hydrogen bonds : bond 0.03257 ( 262) hydrogen bonds : angle 7.11210 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 177 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8485 (m-10) cc_final: 0.8220 (m-10) REVERT: A 163 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8268 (tttm) REVERT: A 168 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8120 (t) REVERT: A 208 LEU cc_start: 0.9144 (tp) cc_final: 0.8898 (pp) REVERT: A 229 ASP cc_start: 0.9690 (p0) cc_final: 0.9429 (p0) REVERT: B 50 LEU cc_start: 0.9124 (mt) cc_final: 0.8907 (mt) REVERT: B 225 ASP cc_start: 0.9222 (p0) cc_final: 0.8995 (p0) REVERT: C 47 ASN cc_start: 0.9180 (t0) cc_final: 0.8776 (t0) REVERT: C 203 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8585 (mm-30) REVERT: C 206 MET cc_start: 0.9440 (pmm) cc_final: 0.9035 (pmm) REVERT: D 151 TYR cc_start: 0.9163 (OUTLIER) cc_final: 0.8878 (p90) REVERT: D 175 TYR cc_start: 0.9405 (m-80) cc_final: 0.8989 (m-80) REVERT: F 1 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8288 (tmm) REVERT: F 23 PHE cc_start: 0.6362 (t80) cc_final: 0.6073 (t80) REVERT: F 28 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8047 (tp-100) REVERT: F 231 MET cc_start: 0.8929 (ppp) cc_final: 0.8652 (ppp) REVERT: G 26 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8609 (tp30) REVERT: G 90 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8589 (t80) REVERT: G 171 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7197 (m-80) REVERT: G 176 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8686 (tmm-80) REVERT: G 206 MET cc_start: 0.8788 (pmm) cc_final: 0.8528 (pmm) REVERT: H 1 MET cc_start: 0.8474 (tpp) cc_final: 0.7641 (tpp) REVERT: H 23 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: H 148 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7642 (p) REVERT: H 206 MET cc_start: 0.9081 (pmm) cc_final: 0.8714 (pmm) REVERT: J 1 MET cc_start: 0.8552 (tmm) cc_final: 0.8024 (tmm) REVERT: J 203 GLU cc_start: 0.8145 (mp0) cc_final: 0.7863 (mp0) REVERT: J 219 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8380 (mmmm) REVERT: K 88 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8924 (mmtm) REVERT: K 113 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8739 (t0) REVERT: K 146 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8867 (ttpp) REVERT: L 1 MET cc_start: 0.8238 (ptm) cc_final: 0.7820 (ptm) REVERT: L 50 LEU cc_start: 0.8995 (mt) cc_final: 0.8621 (mt) REVERT: M 212 ASN cc_start: 0.9537 (t0) cc_final: 0.9148 (t0) REVERT: M 231 MET cc_start: 0.9136 (mtp) cc_final: 0.7372 (mmm) REVERT: M 239 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7368 (tpm170) REVERT: N 152 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.8792 (mp10) REVERT: N 231 MET cc_start: 0.9564 (OUTLIER) cc_final: 0.8852 (mmp) REVERT: O 201 SER cc_start: 0.5210 (OUTLIER) cc_final: 0.4641 (t) outliers start: 134 outliers final: 106 residues processed: 294 average time/residue: 0.1602 time to fit residues: 74.8897 Evaluate side-chains 300 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 176 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 12 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 TYR Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 176 ARG Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 90 PHE Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain H residue 23 PHE Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 65 ASN Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 171 TYR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 204 PHE Chi-restraints excluded: chain O residue 208 LEU Chi-restraints excluded: chain O residue 234 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 63 optimal weight: 30.0000 chunk 84 optimal weight: 50.0000 chunk 171 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 299 optimal weight: 8.9990 chunk 183 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 47 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.051061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.038513 restraints weight = 225994.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.039511 restraints weight = 139379.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040192 restraints weight = 101040.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.040662 restraints weight = 80647.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.040982 restraints weight = 69093.977| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26033 Z= 0.210 Angle : 0.688 14.057 35130 Z= 0.349 Chirality : 0.045 0.263 4008 Planarity : 0.004 0.074 4506 Dihedral : 5.375 26.454 3452 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.89 % Favored : 87.80 % Rotamer: Outliers : 4.93 % Allowed : 32.58 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.14), residues: 3171 helix: -2.12 (0.53), residues: 76 sheet: -0.82 (0.15), residues: 1276 loop : -2.30 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 42 TYR 0.030 0.001 TYR A 51 PHE 0.024 0.002 PHE J 23 TRP 0.034 0.003 TRP L 72 HIS 0.002 0.001 HIS O 94 Details of bonding type rmsd covalent geometry : bond 0.00454 (26033) covalent geometry : angle 0.68813 (35130) hydrogen bonds : bond 0.03524 ( 262) hydrogen bonds : angle 7.33779 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 167 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8264 (tttm) REVERT: A 168 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8189 (t) REVERT: A 170 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5663 (mmm160) REVERT: A 208 LEU cc_start: 0.9171 (tp) cc_final: 0.8924 (pp) REVERT: B 23 PHE cc_start: 0.9110 (t80) cc_final: 0.8811 (t80) REVERT: B 50 LEU cc_start: 0.9162 (mt) cc_final: 0.8889 (mt) REVERT: B 225 ASP cc_start: 0.9186 (p0) cc_final: 0.8976 (p0) REVERT: C 47 ASN cc_start: 0.9161 (t0) cc_final: 0.8783 (t0) REVERT: C 203 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8576 (mm-30) REVERT: C 206 MET cc_start: 0.9424 (pmm) cc_final: 0.9059 (pmm) REVERT: D 151 TYR cc_start: 0.9201 (OUTLIER) cc_final: 0.8927 (p90) REVERT: D 175 TYR cc_start: 0.9480 (m-80) cc_final: 0.9031 (m-80) REVERT: F 1 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8279 (tmm) REVERT: F 23 PHE cc_start: 0.6486 (t80) cc_final: 0.6181 (t80) REVERT: F 28 GLN cc_start: 0.8629 (tm-30) cc_final: 0.7999 (tp-100) REVERT: F 231 MET cc_start: 0.8941 (ppp) cc_final: 0.8215 (ppp) REVERT: G 90 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8676 (t80) REVERT: G 171 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7525 (m-80) REVERT: G 176 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8761 (tmm-80) REVERT: H 1 MET cc_start: 0.8497 (tpp) cc_final: 0.7593 (tpp) REVERT: H 206 MET cc_start: 0.9069 (pmm) cc_final: 0.8602 (pmm) REVERT: H 219 LYS cc_start: 0.9361 (mtpp) cc_final: 0.9160 (mtpp) REVERT: J 1 MET cc_start: 0.8624 (tmm) cc_final: 0.8077 (tmm) REVERT: K 75 MET cc_start: 0.9487 (ptp) cc_final: 0.9103 (pmm) REVERT: K 88 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8862 (mmtm) REVERT: K 113 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8736 (t0) REVERT: K 146 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8902 (tmtt) REVERT: L 1 MET cc_start: 0.8308 (ptm) cc_final: 0.7876 (ptm) REVERT: M 212 ASN cc_start: 0.9550 (t0) cc_final: 0.9170 (t0) REVERT: M 231 MET cc_start: 0.9132 (mtp) cc_final: 0.7989 (mmm) REVERT: M 239 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7305 (tpm170) REVERT: N 148 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8203 (t) REVERT: N 152 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.8802 (mp10) REVERT: N 231 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.8834 (mmp) REVERT: O 166 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7529 (pptt) REVERT: O 176 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8275 (tmm-80) REVERT: O 201 SER cc_start: 0.5736 (OUTLIER) cc_final: 0.5181 (t) outliers start: 137 outliers final: 108 residues processed: 291 average time/residue: 0.1672 time to fit residues: 77.2378 Evaluate side-chains 292 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 165 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 12 TYR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 90 PHE Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 176 ARG Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 90 PHE Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 176 ARG Chi-restraints excluded: chain G residue 234 VAL Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 206 MET Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 205 GLU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 229 ASP Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 239 ARG Chi-restraints excluded: chain N residue 2 LYS Chi-restraints excluded: chain N residue 41 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 148 THR Chi-restraints excluded: chain N residue 152 GLN Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 167 PHE Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain O residue 65 ASN Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 166 LYS Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 171 TYR Chi-restraints excluded: chain O residue 176 ARG Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 204 PHE Chi-restraints excluded: chain O residue 208 LEU Chi-restraints excluded: chain O residue 234 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 211 optimal weight: 40.0000 chunk 59 optimal weight: 0.2980 chunk 77 optimal weight: 30.0000 chunk 289 optimal weight: 20.0000 chunk 282 optimal weight: 30.0000 chunk 78 optimal weight: 0.9990 chunk 314 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 297 optimal weight: 8.9990 chunk 291 optimal weight: 4.9990 chunk 215 optimal weight: 50.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 47 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** J 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.052073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.039327 restraints weight = 216142.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.040388 restraints weight = 131476.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.041104 restraints weight = 94216.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041605 restraints weight = 74849.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.041920 restraints weight = 63639.429| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26033 Z= 0.135 Angle : 0.659 14.008 35130 Z= 0.330 Chirality : 0.045 0.264 4008 Planarity : 0.003 0.064 4506 Dihedral : 5.138 25.411 3452 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.56 % Favored : 89.12 % Rotamer: Outliers : 4.75 % Allowed : 32.61 % Favored : 62.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.14), residues: 3171 helix: -1.91 (0.57), residues: 64 sheet: -0.73 (0.15), residues: 1263 loop : -2.21 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 42 TYR 0.022 0.001 TYR A 51 PHE 0.029 0.001 PHE J 23 TRP 0.033 0.002 TRP L 72 HIS 0.001 0.000 HIS F 94 Details of bonding type rmsd covalent geometry : bond 0.00302 (26033) covalent geometry : angle 0.65898 (35130) hydrogen bonds : bond 0.03177 ( 262) hydrogen bonds : angle 7.15086 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4529.75 seconds wall clock time: 79 minutes 47.60 seconds (4787.60 seconds total)