Starting phenix.real_space_refine on Thu Feb 5 04:30:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7og5_12878/02_2026/7og5_12878.cif Found real_map, /net/cci-nas-00/data/ceres_data/7og5_12878/02_2026/7og5_12878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7og5_12878/02_2026/7og5_12878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7og5_12878/02_2026/7og5_12878.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7og5_12878/02_2026/7og5_12878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7og5_12878/02_2026/7og5_12878.map" } resolution = 3.37 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= 0.002 sd= 0.032 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 96 5.16 5 C 9796 2.51 5 N 2675 2.21 5 O 2877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15444 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "J" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1376 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain breaks: 1 Chain: "F" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "B" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "D" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "L" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1274 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Chain: "E" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "C" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "G" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "K" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "I" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "A" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1274 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Time building chain proxies: 3.64, per 1000 atoms: 0.24 Number of scatterers: 15444 At special positions: 0 Unit cell: (106.624, 119.119, 126.616, 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 96 16.00 O 2877 8.00 N 2675 7.00 C 9796 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: 1.46 Conformation dependent library (CDL) restraints added in 615.4 milliseconds 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3614 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 14 sheets defined 65.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'H' and resid 7 through 12 Processing helix chain 'H' and resid 23 through 35 Processing helix chain 'H' and resid 45 through 56 Processing helix chain 'H' and resid 58 through 68 removed outlier: 4.304A pdb=" N GLU H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 96 removed outlier: 4.225A pdb=" N LEU H 86 " --> pdb=" O PRO H 82 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR H 87 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU H 91 " --> pdb=" O TYR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 154 removed outlier: 3.662A pdb=" N GLY H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 172 Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'H' and resid 180 through 186 Processing helix chain 'J' and resid 7 through 12 Processing helix chain 'J' and resid 23 through 35 Processing helix chain 'J' and resid 45 through 56 Processing helix chain 'J' and resid 58 through 69 removed outlier: 4.195A pdb=" N ALA J 63 " --> pdb=" O ASP J 59 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLU J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 102 removed outlier: 4.020A pdb=" N TYR J 87 " --> pdb=" O SER J 83 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE J 97 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN J 98 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 154 removed outlier: 3.938A pdb=" N ALA J 132 " --> pdb=" O ARG J 128 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET J 133 " --> pdb=" O TYR J 129 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG J 141 " --> pdb=" O ILE J 137 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 177 through 179 No H-bonds generated for 'chain 'J' and resid 177 through 179' Processing helix chain 'J' and resid 180 through 186 Processing helix chain 'F' and resid 8 through 12 Processing helix chain 'F' and resid 23 through 35 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 61 through 68 Processing helix chain 'F' and resid 83 through 96 removed outlier: 4.133A pdb=" N TYR F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 154 Processing helix chain 'F' and resid 161 through 172 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 180 through 187 Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.057A pdb=" N PHE B 11 " --> pdb=" O ASP B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.541A pdb=" N GLU B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 154 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 180 through 186 Processing helix chain 'D' and resid 7 through 13 removed outlier: 3.876A pdb=" N PHE D 11 " --> pdb=" O ASP D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 18 removed outlier: 3.787A pdb=" N TYR D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU D 18 " --> pdb=" O PRO D 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 13 through 18' Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 58 through 68 removed outlier: 4.701A pdb=" N GLU D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 96 removed outlier: 3.624A pdb=" N TYR D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 91 " --> pdb=" O TYR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 154 removed outlier: 3.529A pdb=" N VAL D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 180 through 188 Processing helix chain 'L' and resid 7 through 12 Processing helix chain 'L' and resid 23 through 35 Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 58 through 68 removed outlier: 3.835A pdb=" N GLU L 64 " --> pdb=" O LEU L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 96 removed outlier: 3.606A pdb=" N GLU L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 154 Processing helix chain 'L' and resid 161 through 172 Processing helix chain 'L' and resid 177 through 186 removed outlier: 4.043A pdb=" N ARG L 182 " --> pdb=" O PRO L 178 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY L 183 " --> pdb=" O ARG L 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 13 removed outlier: 4.103A pdb=" N PHE E 11 " --> pdb=" O ASP E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 18 Processing helix chain 'E' and resid 23 through 35 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 58 through 68 removed outlier: 4.688A pdb=" N GLU E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 95 removed outlier: 3.719A pdb=" N TYR E 87 " --> pdb=" O SER E 83 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 153 Processing helix chain 'E' and resid 161 through 172 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 58 through 68 removed outlier: 4.081A pdb=" N ALA C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 96 removed outlier: 3.975A pdb=" N TYR C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 153 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 180 through 188 Processing helix chain 'G' and resid 7 through 13 removed outlier: 4.020A pdb=" N PHE G 11 " --> pdb=" O ASP G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 35 Processing helix chain 'G' and resid 45 through 56 Processing helix chain 'G' and resid 58 through 68 removed outlier: 3.687A pdb=" N ALA G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 96 removed outlier: 3.888A pdb=" N TYR G 87 " --> pdb=" O SER G 83 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU G 91 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU G 92 " --> pdb=" O GLU G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 154 Processing helix chain 'G' and resid 161 through 172 Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'K' and resid 8 through 13 Processing helix chain 'K' and resid 23 through 35 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.936A pdb=" N GLU K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 96 Processing helix chain 'K' and resid 132 through 154 Processing helix chain 'K' and resid 161 through 172 Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 180 through 186 removed outlier: 3.629A pdb=" N GLN K 186 " --> pdb=" O ARG K 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 13 Processing helix chain 'I' and resid 13 through 18 Processing helix chain 'I' and resid 23 through 35 Processing helix chain 'I' and resid 45 through 56 removed outlier: 3.551A pdb=" N LEU I 55 " --> pdb=" O GLU I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 68 removed outlier: 4.016A pdb=" N ALA I 63 " --> pdb=" O ASP I 59 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 96 removed outlier: 4.163A pdb=" N LEU I 86 " --> pdb=" O PRO I 82 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR I 87 " --> pdb=" O SER I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.123A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE I 137 " --> pdb=" O MET I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 172 Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 180 through 187 Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.805A pdb=" N LEU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 68 removed outlier: 4.243A pdb=" N ALA A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 96 removed outlier: 4.293A pdb=" N TYR A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 154 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.919A pdb=" N GLY A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 5 removed outlier: 6.570A pdb=" N PHE H 4 " --> pdb=" O TYR H 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 174 through 175 removed outlier: 4.148A pdb=" N ILE J 71 " --> pdb=" O LEU H 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 41 through 43 removed outlier: 6.490A pdb=" N PHE J 4 " --> pdb=" O TYR J 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 71 removed outlier: 8.788A pdb=" N TYR B 70 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE B 42 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG B 3 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 82 Processing sheet with id=AA7, first strand: chain 'D' and resid 70 through 71 removed outlier: 6.804A pdb=" N PHE D 42 " --> pdb=" O TYR D 70 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE D 4 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 80 through 82 Processing sheet with id=AA9, first strand: chain 'L' and resid 69 through 71 removed outlier: 6.567A pdb=" N PHE L 4 " --> pdb=" O TYR L 43 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG L 3 " --> pdb=" O THR L 156 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL L 158 " --> pdb=" O ARG L 3 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL L 5 " --> pdb=" O VAL L 158 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU L 157 " --> pdb=" O VAL L 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 80 through 82 removed outlier: 3.603A pdb=" N ILE L 81 " --> pdb=" O ILE K 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 174 through 175 removed outlier: 6.812A pdb=" N ARG C 2 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N TYR C 43 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE C 4 " --> pdb=" O TYR C 43 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N TYR C 70 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE C 42 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARG C 72 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 71 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG E 2 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N TYR E 43 " --> pdb=" O ARG E 2 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE E 4 " --> pdb=" O TYR E 43 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N TYR E 70 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE E 42 " --> pdb=" O TYR E 70 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG E 72 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE E 71 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS G 174 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE G 4 " --> pdb=" O TYR G 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 70 through 71 removed outlier: 8.292A pdb=" N TYR K 70 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE K 42 " --> pdb=" O TYR K 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU K 41 " --> pdb=" O ARG K 2 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU K 157 " --> pdb=" O VAL K 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 69 through 71 removed outlier: 6.689A pdb=" N PHE I 42 " --> pdb=" O TYR I 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.672A pdb=" N PHE A 42 " --> pdb=" O TYR A 70 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG A 3 " --> pdb=" O THR A 156 " (cutoff:3.500A) 817 hydrogen bonds defined for protein. 2385 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.90 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: 5188 1.34 - 1.46: 2665 1.46 - 1.58: 7664 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 15697 Sorted by residual: bond pdb=" CG LEU G 149 " pdb=" CD2 LEU G 149 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.78e+00 bond pdb=" CG LEU H 149 " pdb=" CD2 LEU H 149 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" C ARG A 72 " pdb=" N SER A 73 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.47e-02 4.63e+03 4.04e+00 bond pdb=" CB ILE H 171 " pdb=" CG2 ILE H 171 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.89e+00 bond pdb=" CB ARG E 72 " pdb=" CG ARG E 72 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.72e+00 ... (remaining 15692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 19797 1.78 - 3.57: 1134 3.57 - 5.35: 189 5.35 - 7.13: 34 7.13 - 8.91: 5 Bond angle restraints: 21159 Sorted by residual: angle pdb=" N VAL J 16 " pdb=" CA VAL J 16 " pdb=" C VAL J 16 " ideal model delta sigma weight residual 113.71 105.90 7.81 9.50e-01 1.11e+00 6.76e+01 angle pdb=" N VAL G 16 " pdb=" CA VAL G 16 " pdb=" C VAL G 16 " ideal model delta sigma weight residual 113.71 107.41 6.30 9.50e-01 1.11e+00 4.40e+01 angle pdb=" N VAL A 16 " pdb=" CA VAL A 16 " pdb=" C VAL A 16 " ideal model delta sigma weight residual 113.71 107.82 5.89 9.50e-01 1.11e+00 3.84e+01 angle pdb=" C VAL H 16 " pdb=" N TYR H 17 " pdb=" CA TYR H 17 " ideal model delta sigma weight residual 120.54 126.22 -5.68 1.35e+00 5.49e-01 1.77e+01 angle pdb=" C VAL F 16 " pdb=" N TYR F 17 " pdb=" CA TYR F 17 " ideal model delta sigma weight residual 122.17 128.31 -6.14 1.54e+00 4.22e-01 1.59e+01 ... (remaining 21154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8622 17.94 - 35.89: 886 35.89 - 53.83: 148 53.83 - 71.77: 19 71.77 - 89.71: 16 Dihedral angle restraints: 9691 sinusoidal: 4124 harmonic: 5567 Sorted by residual: dihedral pdb=" CA MET J 185 " pdb=" C MET J 185 " pdb=" N GLN J 186 " pdb=" CA GLN J 186 " ideal model delta harmonic sigma weight residual 180.00 148.74 31.26 0 5.00e+00 4.00e-02 3.91e+01 dihedral pdb=" CA TYR E 17 " pdb=" C TYR E 17 " pdb=" N LEU E 18 " pdb=" CA LEU E 18 " ideal model delta harmonic sigma weight residual 180.00 152.29 27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ARG C 75 " pdb=" C ARG C 75 " pdb=" N ARG C 76 " pdb=" CA ARG C 76 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 9688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1851 0.060 - 0.120: 449 0.120 - 0.180: 44 0.180 - 0.240: 4 0.240 - 0.300: 1 Chirality restraints: 2349 Sorted by residual: chirality pdb=" CG LEU H 149 " pdb=" CB LEU H 149 " pdb=" CD1 LEU H 149 " pdb=" CD2 LEU H 149 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA PRO I 24 " pdb=" N PRO I 24 " pdb=" C PRO I 24 " pdb=" CB PRO I 24 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CG LEU A 86 " pdb=" CB LEU A 86 " pdb=" CD1 LEU A 86 " pdb=" CD2 LEU A 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.25e-01 ... (remaining 2346 not shown) Planarity restraints: 2775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 13 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO E 14 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 81 " -0.049 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO J 82 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO J 82 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO J 82 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 142 " 0.014 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C GLU D 142 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU D 142 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP D 143 " 0.016 2.00e-02 2.50e+03 ... (remaining 2772 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 197 2.60 - 3.17: 15063 3.17 - 3.75: 23897 3.75 - 4.32: 33260 4.32 - 4.90: 54081 Nonbonded interactions: 126498 Sorted by model distance: nonbonded pdb=" O MET L 79 " pdb=" OG SER K 83 " model vdw 2.021 3.040 nonbonded pdb=" OG SER H 83 " pdb=" O MET G 79 " model vdw 2.035 3.040 nonbonded pdb=" O ARG F 76 " pdb=" OG SER E 83 " model vdw 2.057 3.040 nonbonded pdb=" OG1 THR D 67 " pdb=" OE1 GLU D 68 " model vdw 2.077 3.040 nonbonded pdb=" OD1 ASP B 145 " pdb=" OH TYR A 87 " model vdw 2.096 3.040 ... (remaining 126493 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' selection = (chain 'B' and resid 2 through 189) selection = (chain 'C' and resid 2 through 189) selection = (chain 'D' and resid 2 through 189) selection = (chain 'E' and resid 2 through 189) selection = (chain 'F' and resid 2 through 189) selection = (chain 'G' and resid 2 through 189) selection = (chain 'H' and resid 2 through 189) selection = (chain 'I' and resid 2 through 189) selection = (chain 'J' and (resid 2 through 98 or resid 131 through 189)) selection = (chain 'K' and resid 2 through 189) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.390 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.010 0.079 15697 Z= 0.431 Angle : 0.951 8.913 21159 Z= 0.541 Chirality : 0.051 0.300 2349 Planarity : 0.006 0.105 2775 Dihedral : 14.710 89.713 6077 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.19), residues: 1844 helix: -0.80 (0.15), residues: 1134 sheet: -1.06 (0.81), residues: 46 loop : -1.27 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 76 TYR 0.036 0.003 TYR G 17 PHE 0.021 0.003 PHE I 89 Details of bonding type rmsd covalent geometry : bond 0.01032 (15697) covalent geometry : angle 0.95071 (21159) hydrogen bonds : bond 0.16903 ( 817) hydrogen bonds : angle 7.55977 ( 2385) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8758 (t70) cc_final: 0.8231 (t0) REVERT: F 84 GLU cc_start: 0.7465 (tm-30) cc_final: 0.6945 (tm-30) REVERT: F 169 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7798 (tm-30) REVERT: B 44 MET cc_start: 0.5881 (tpt) cc_final: 0.5553 (tpt) REVERT: B 166 LYS cc_start: 0.8311 (tppp) cc_final: 0.7832 (tttt) REVERT: D 39 ASP cc_start: 0.8634 (t70) cc_final: 0.8393 (t0) REVERT: L 53 CYS cc_start: 0.5347 (t) cc_final: 0.5135 (t) REVERT: L 174 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7023 (tttt) REVERT: E 7 ASP cc_start: 0.8183 (t0) cc_final: 0.7963 (t0) REVERT: E 50 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7995 (tp-100) REVERT: C 7 ASP cc_start: 0.8367 (t0) cc_final: 0.7963 (t70) REVERT: C 187 ASN cc_start: 0.8007 (m110) cc_final: 0.7600 (m110) REVERT: K 1 SER cc_start: 0.8229 (p) cc_final: 0.7855 (p) REVERT: K 7 ASP cc_start: 0.7622 (t0) cc_final: 0.7179 (t0) REVERT: K 25 MET cc_start: 0.5691 (mmt) cc_final: 0.4724 (ttp) REVERT: K 39 ASP cc_start: 0.7858 (t70) cc_final: 0.7477 (t0) REVERT: K 161 ASP cc_start: 0.7176 (m-30) cc_final: 0.6917 (m-30) REVERT: K 171 ILE cc_start: 0.8748 (tt) cc_final: 0.8529 (tt) REVERT: I 39 ASP cc_start: 0.7412 (t0) cc_final: 0.7131 (t0) REVERT: A 89 PHE cc_start: 0.8043 (t80) cc_final: 0.7824 (t80) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1096 time to fit residues: 74.0408 Evaluate side-chains 385 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 ASN H 187 ASN B 54 ASN G 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.181330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128013 restraints weight = 21142.099| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.04 r_work: 0.3385 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15697 Z= 0.144 Angle : 0.664 12.565 21159 Z= 0.350 Chirality : 0.043 0.194 2349 Planarity : 0.005 0.072 2775 Dihedral : 5.332 23.769 2174 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.85 % Allowed : 10.33 % Favored : 87.82 % 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 are not related in a simple way. whole: -0.55 (0.20), residues: 1844 helix: 0.04 (0.15), residues: 1173 sheet: -0.46 (0.46), residues: 136 loop : -0.95 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 76 TYR 0.032 0.002 TYR G 17 PHE 0.025 0.001 PHE I 89 Details of bonding type rmsd covalent geometry : bond 0.00326 (15697) covalent geometry : angle 0.66404 (21159) hydrogen bonds : bond 0.04211 ( 817) hydrogen bonds : angle 5.11229 ( 2385) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 462 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8768 (t70) cc_final: 0.8173 (t70) REVERT: J 79 MET cc_start: 0.8913 (ttp) cc_final: 0.8651 (ttp) REVERT: J 84 GLU cc_start: 0.9041 (tp30) cc_final: 0.8723 (tp30) REVERT: J 154 ASP cc_start: 0.8790 (t0) cc_final: 0.8547 (t0) REVERT: J 169 GLU cc_start: 0.8531 (tt0) cc_final: 0.7995 (pt0) REVERT: F 68 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: F 169 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7799 (tm-30) REVERT: B 84 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6922 (pp20) REVERT: B 148 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6603 (mt) REVERT: B 166 LYS cc_start: 0.8142 (tppp) cc_final: 0.7718 (tttt) REVERT: D 39 ASP cc_start: 0.8691 (t70) cc_final: 0.8346 (t0) REVERT: D 66 GLU cc_start: 0.8922 (tt0) cc_final: 0.8689 (tt0) REVERT: D 84 GLU cc_start: 0.8277 (tp30) cc_final: 0.7754 (tp30) REVERT: L 34 LEU cc_start: 0.8498 (mm) cc_final: 0.8218 (mm) REVERT: L 41 GLU cc_start: 0.7834 (pt0) cc_final: 0.7490 (pm20) REVERT: E 26 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8326 (tm-30) REVERT: E 39 ASP cc_start: 0.9059 (t70) cc_final: 0.8378 (t0) REVERT: E 50 GLN cc_start: 0.8311 (tp-100) cc_final: 0.8037 (tp-100) REVERT: E 138 LEU cc_start: 0.8384 (tp) cc_final: 0.8157 (tp) REVERT: C 21 ASP cc_start: 0.7055 (t70) cc_final: 0.6840 (t0) REVERT: C 26 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8261 (mm-40) REVERT: C 39 ASP cc_start: 0.8678 (t70) cc_final: 0.8386 (t70) REVERT: C 133 MET cc_start: 0.2069 (ttm) cc_final: 0.1841 (mtt) REVERT: C 137 ILE cc_start: 0.7553 (mt) cc_final: 0.7252 (mp) REVERT: C 186 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7131 (mt0) REVERT: G 162 GLU cc_start: 0.8265 (tp30) cc_final: 0.7993 (tp30) REVERT: K 1 SER cc_start: 0.7859 (p) cc_final: 0.7438 (p) REVERT: K 25 MET cc_start: 0.5413 (mmt) cc_final: 0.4420 (ttp) REVERT: K 39 ASP cc_start: 0.8013 (t70) cc_final: 0.7527 (t0) REVERT: K 75 ARG cc_start: 0.6896 (tpt170) cc_final: 0.6666 (tpt170) REVERT: K 96 ARG cc_start: 0.6745 (mpt90) cc_final: 0.6387 (mmp-170) REVERT: K 161 ASP cc_start: 0.7088 (m-30) cc_final: 0.6788 (m-30) REVERT: K 166 LYS cc_start: 0.8531 (mppt) cc_final: 0.8064 (mppt) REVERT: I 13 ASN cc_start: 0.8498 (t0) cc_final: 0.8247 (t0) REVERT: I 16 VAL cc_start: 0.8129 (p) cc_final: 0.7803 (p) REVERT: I 17 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.5275 (t80) REVERT: I 21 ASP cc_start: 0.7500 (t70) cc_final: 0.7022 (t70) REVERT: I 39 ASP cc_start: 0.7678 (t0) cc_final: 0.7395 (t0) REVERT: I 169 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8062 (tm-30) REVERT: I 187 ASN cc_start: 0.8694 (m-40) cc_final: 0.8364 (m110) outliers start: 31 outliers final: 10 residues processed: 472 average time/residue: 0.1237 time to fit residues: 88.0717 Evaluate side-chains 421 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 406 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 2 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 ASN H 187 ASN C 50 GLN K 26 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.171596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117494 restraints weight = 21560.289| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.96 r_work: 0.3246 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 15697 Z= 0.326 Angle : 0.765 12.048 21159 Z= 0.398 Chirality : 0.046 0.190 2349 Planarity : 0.006 0.063 2775 Dihedral : 5.477 26.622 2174 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.06 % Allowed : 15.46 % Favored : 80.48 % 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 are not related in a simple way. whole: -0.54 (0.20), residues: 1844 helix: 0.27 (0.16), residues: 1106 sheet: -1.14 (0.37), residues: 190 loop : -1.11 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 182 TYR 0.032 0.002 TYR G 17 PHE 0.026 0.002 PHE C 89 Details of bonding type rmsd covalent geometry : bond 0.00808 (15697) covalent geometry : angle 0.76504 (21159) hydrogen bonds : bond 0.04647 ( 817) hydrogen bonds : angle 5.20165 ( 2385) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 413 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8969 (t70) cc_final: 0.8454 (t0) REVERT: H 86 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7521 (tt) REVERT: J 154 ASP cc_start: 0.8895 (t0) cc_final: 0.8485 (t0) REVERT: J 174 LYS cc_start: 0.8413 (mttt) cc_final: 0.8119 (mttt) REVERT: F 17 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.7298 (t80) REVERT: F 32 LEU cc_start: 0.9186 (mt) cc_final: 0.8876 (mt) REVERT: F 68 GLU cc_start: 0.8265 (pm20) cc_final: 0.7924 (pm20) REVERT: F 162 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7951 (tm-30) REVERT: F 169 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7836 (tm-30) REVERT: F 185 MET cc_start: 0.8877 (mpp) cc_final: 0.8177 (mtm) REVERT: B 84 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6930 (pp20) REVERT: B 166 LYS cc_start: 0.8176 (tppp) cc_final: 0.7807 (tttt) REVERT: D 39 ASP cc_start: 0.8821 (t70) cc_final: 0.8291 (t70) REVERT: D 84 GLU cc_start: 0.8436 (tp30) cc_final: 0.7865 (tp30) REVERT: L 29 SER cc_start: 0.8735 (t) cc_final: 0.8256 (p) REVERT: L 34 LEU cc_start: 0.8554 (mm) cc_final: 0.8215 (mm) REVERT: L 164 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6811 (mmm) REVERT: L 181 LEU cc_start: 0.8441 (tp) cc_final: 0.8227 (tp) REVERT: E 26 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8593 (tm-30) REVERT: E 39 ASP cc_start: 0.9176 (t70) cc_final: 0.8477 (t0) REVERT: E 50 GLN cc_start: 0.8383 (tp-100) cc_final: 0.8063 (tp-100) REVERT: E 154 ASP cc_start: 0.9163 (t0) cc_final: 0.8948 (t0) REVERT: E 164 MET cc_start: 0.8864 (tpp) cc_final: 0.8489 (ttm) REVERT: C 21 ASP cc_start: 0.7180 (t70) cc_final: 0.6969 (t0) REVERT: C 39 ASP cc_start: 0.8937 (t70) cc_final: 0.8599 (t70) REVERT: C 186 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7007 (mt0) REVERT: G 50 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8152 (tm-30) REVERT: G 133 MET cc_start: 0.7574 (pmm) cc_final: 0.7148 (pmm) REVERT: G 134 ARG cc_start: 0.5732 (mpt180) cc_final: 0.5337 (mmt180) REVERT: K 1 SER cc_start: 0.7978 (p) cc_final: 0.7562 (p) REVERT: K 25 MET cc_start: 0.5490 (mmt) cc_final: 0.4603 (ttp) REVERT: K 39 ASP cc_start: 0.8008 (t70) cc_final: 0.7556 (t0) REVERT: K 75 ARG cc_start: 0.6946 (tpt170) cc_final: 0.6685 (tpt170) REVERT: K 161 ASP cc_start: 0.6983 (m-30) cc_final: 0.6771 (m-30) REVERT: K 166 LYS cc_start: 0.8463 (mppt) cc_final: 0.8019 (mppt) REVERT: K 173 ILE cc_start: 0.8854 (mt) cc_final: 0.8180 (tt) REVERT: I 17 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.5613 (t80) REVERT: I 21 ASP cc_start: 0.7564 (t70) cc_final: 0.7150 (t70) REVERT: I 25 MET cc_start: 0.8234 (mmm) cc_final: 0.7984 (tpp) REVERT: I 39 ASP cc_start: 0.7879 (t0) cc_final: 0.7575 (t0) REVERT: I 51 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8633 (tm-30) REVERT: A 164 MET cc_start: 0.8241 (ttt) cc_final: 0.7920 (ttm) outliers start: 68 outliers final: 35 residues processed: 441 average time/residue: 0.1228 time to fit residues: 82.7341 Evaluate side-chains 432 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 391 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 186 GLN Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 160 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 ASN H 187 ASN K 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.179572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125923 restraints weight = 21404.474| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.05 r_work: 0.3363 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15697 Z= 0.143 Angle : 0.630 13.232 21159 Z= 0.327 Chirality : 0.042 0.247 2349 Planarity : 0.005 0.057 2775 Dihedral : 4.906 23.569 2174 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.76 % Allowed : 16.84 % Favored : 79.40 % 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 are not related in a simple way. whole: -0.03 (0.21), residues: 1844 helix: 0.64 (0.16), residues: 1108 sheet: -0.93 (0.38), residues: 190 loop : -0.82 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 96 TYR 0.024 0.001 TYR E 17 PHE 0.026 0.001 PHE H 89 Details of bonding type rmsd covalent geometry : bond 0.00336 (15697) covalent geometry : angle 0.62981 (21159) hydrogen bonds : bond 0.03644 ( 817) hydrogen bonds : angle 4.66980 ( 2385) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 439 time to evaluate : 0.663 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: H 39 ASP cc_start: 0.8805 (t70) cc_final: 0.8229 (t70) REVERT: H 144 ILE cc_start: 0.8761 (tp) cc_final: 0.8508 (tp) REVERT: J 154 ASP cc_start: 0.8805 (t0) cc_final: 0.8419 (t0) REVERT: J 174 LYS cc_start: 0.8381 (mttt) cc_final: 0.8047 (mttt) REVERT: F 17 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.7072 (t80) REVERT: F 32 LEU cc_start: 0.9132 (mt) cc_final: 0.8838 (mt) REVERT: F 44 MET cc_start: 0.8230 (ttm) cc_final: 0.7902 (ttp) REVERT: F 68 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: F 84 GLU cc_start: 0.7828 (tp30) cc_final: 0.7482 (tp30) REVERT: F 169 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 166 LYS cc_start: 0.8131 (tppp) cc_final: 0.7818 (tttt) REVERT: D 39 ASP cc_start: 0.8665 (t70) cc_final: 0.8379 (t0) REVERT: D 84 GLU cc_start: 0.8416 (tp30) cc_final: 0.7715 (tp30) REVERT: L 29 SER cc_start: 0.8738 (t) cc_final: 0.8246 (p) REVERT: L 34 LEU cc_start: 0.8470 (mm) cc_final: 0.8121 (mm) REVERT: E 26 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8346 (tm-30) REVERT: E 39 ASP cc_start: 0.9089 (t70) cc_final: 0.8250 (t0) REVERT: E 50 GLN cc_start: 0.8286 (tp-100) cc_final: 0.8044 (tp-100) REVERT: E 138 LEU cc_start: 0.8394 (tp) cc_final: 0.8167 (tp) REVERT: E 151 TYR cc_start: 0.9363 (t80) cc_final: 0.9151 (t80) REVERT: E 177 ASN cc_start: 0.8883 (t0) cc_final: 0.8676 (t0) REVERT: C 21 ASP cc_start: 0.6954 (t70) cc_final: 0.6664 (t0) REVERT: C 26 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8145 (mm-40) REVERT: C 39 ASP cc_start: 0.8819 (t70) cc_final: 0.8369 (t70) REVERT: C 137 ILE cc_start: 0.7582 (mt) cc_final: 0.7304 (mp) REVERT: C 186 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6938 (mt0) REVERT: G 86 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8156 (tt) REVERT: G 134 ARG cc_start: 0.5833 (mpt180) cc_final: 0.5381 (mmt90) REVERT: G 162 GLU cc_start: 0.8369 (tp30) cc_final: 0.8026 (tp30) REVERT: K 1 SER cc_start: 0.7964 (p) cc_final: 0.7624 (p) REVERT: K 25 MET cc_start: 0.5399 (mmt) cc_final: 0.4629 (ttp) REVERT: K 39 ASP cc_start: 0.8001 (t70) cc_final: 0.7508 (t0) REVERT: K 52 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6810 (pp) REVERT: K 75 ARG cc_start: 0.6896 (tpt170) cc_final: 0.6643 (tpt170) REVERT: K 161 ASP cc_start: 0.7029 (m-30) cc_final: 0.6798 (m-30) REVERT: K 166 LYS cc_start: 0.8452 (mppt) cc_final: 0.8105 (mppt) REVERT: K 173 ILE cc_start: 0.8770 (mt) cc_final: 0.8280 (tt) REVERT: I 13 ASN cc_start: 0.8471 (t0) cc_final: 0.8170 (t0) REVERT: I 17 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.5924 (t80) REVERT: I 21 ASP cc_start: 0.7395 (t70) cc_final: 0.6889 (t70) REVERT: I 25 MET cc_start: 0.7762 (mmm) cc_final: 0.6852 (ptm) REVERT: I 39 ASP cc_start: 0.7660 (t0) cc_final: 0.7382 (t0) REVERT: I 51 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8508 (tm-30) REVERT: I 169 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 145 ASP cc_start: 0.7650 (m-30) cc_final: 0.7299 (m-30) outliers start: 63 outliers final: 31 residues processed: 467 average time/residue: 0.1265 time to fit residues: 89.4869 Evaluate side-chains 444 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 407 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 96 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 187 ASN L 187 ASN C 187 ASN K 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.178040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124045 restraints weight = 21307.963| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.03 r_work: 0.3336 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15697 Z= 0.168 Angle : 0.656 13.291 21159 Z= 0.335 Chirality : 0.042 0.197 2349 Planarity : 0.005 0.057 2775 Dihedral : 4.822 23.712 2174 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.46 % Allowed : 18.75 % Favored : 77.79 % 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 are not related in a simple way. whole: 0.09 (0.21), residues: 1844 helix: 0.68 (0.16), residues: 1108 sheet: -0.89 (0.38), residues: 190 loop : -0.65 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 96 TYR 0.024 0.002 TYR E 17 PHE 0.025 0.001 PHE A 89 Details of bonding type rmsd covalent geometry : bond 0.00412 (15697) covalent geometry : angle 0.65595 (21159) hydrogen bonds : bond 0.03699 ( 817) hydrogen bonds : angle 4.64570 ( 2385) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 423 time to evaluate : 0.621 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: H 39 ASP cc_start: 0.8819 (t70) cc_final: 0.8285 (t70) REVERT: H 86 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7598 (tt) REVERT: H 144 ILE cc_start: 0.8788 (tp) cc_final: 0.8497 (tp) REVERT: J 51 GLU cc_start: 0.8280 (pp20) cc_final: 0.8026 (pp20) REVERT: J 174 LYS cc_start: 0.8437 (mttt) cc_final: 0.7756 (mtpt) REVERT: F 17 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.7072 (t80) REVERT: F 84 GLU cc_start: 0.7960 (tp30) cc_final: 0.7611 (tp30) REVERT: F 169 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7747 (tm-30) REVERT: B 166 LYS cc_start: 0.8141 (tppp) cc_final: 0.7819 (tttt) REVERT: D 25 MET cc_start: 0.5315 (tpp) cc_final: 0.4967 (tpp) REVERT: D 39 ASP cc_start: 0.8727 (t70) cc_final: 0.8437 (t0) REVERT: L 29 SER cc_start: 0.8753 (t) cc_final: 0.8253 (p) REVERT: L 34 LEU cc_start: 0.8485 (mm) cc_final: 0.8261 (mm) REVERT: E 26 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8393 (tm-30) REVERT: E 39 ASP cc_start: 0.9079 (t70) cc_final: 0.8265 (t0) REVERT: E 50 GLN cc_start: 0.8206 (tp-100) cc_final: 0.7977 (tp-100) REVERT: E 138 LEU cc_start: 0.8412 (tp) cc_final: 0.8172 (tp) REVERT: E 164 MET cc_start: 0.8784 (tpp) cc_final: 0.8086 (ttm) REVERT: E 177 ASN cc_start: 0.8899 (t0) cc_final: 0.8685 (t0) REVERT: C 21 ASP cc_start: 0.7067 (t70) cc_final: 0.6724 (t0) REVERT: C 26 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8132 (mm-40) REVERT: C 39 ASP cc_start: 0.8885 (t70) cc_final: 0.8406 (t70) REVERT: C 137 ILE cc_start: 0.7605 (mt) cc_final: 0.7323 (mp) REVERT: C 186 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6925 (mt0) REVERT: G 86 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8128 (tt) REVERT: K 1 SER cc_start: 0.8024 (p) cc_final: 0.7725 (p) REVERT: K 25 MET cc_start: 0.5316 (mmt) cc_final: 0.4486 (ttp) REVERT: K 39 ASP cc_start: 0.7983 (t70) cc_final: 0.7499 (t0) REVERT: K 52 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6791 (pp) REVERT: K 162 GLU cc_start: 0.7759 (mp0) cc_final: 0.7446 (mp0) REVERT: K 166 LYS cc_start: 0.8463 (mppt) cc_final: 0.8094 (mppt) REVERT: K 173 ILE cc_start: 0.8753 (mt) cc_final: 0.8259 (tt) REVERT: I 13 ASN cc_start: 0.8544 (t0) cc_final: 0.8238 (t0) REVERT: I 17 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6053 (t80) REVERT: I 21 ASP cc_start: 0.7420 (t70) cc_final: 0.6948 (t70) REVERT: I 39 ASP cc_start: 0.7682 (t0) cc_final: 0.7429 (t0) REVERT: I 51 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8501 (tm-30) REVERT: I 70 TYR cc_start: 0.8805 (m-10) cc_final: 0.8289 (m-10) REVERT: I 89 PHE cc_start: 0.8885 (t80) cc_final: 0.8620 (t80) REVERT: I 161 ASP cc_start: 0.7756 (t0) cc_final: 0.7464 (t0) REVERT: A 96 ARG cc_start: 0.6754 (mtt90) cc_final: 0.5897 (ttp80) REVERT: A 164 MET cc_start: 0.8064 (ttt) cc_final: 0.7464 (mtt) outliers start: 58 outliers final: 35 residues processed: 450 average time/residue: 0.1246 time to fit residues: 85.1415 Evaluate side-chains 442 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 401 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 19 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 ASN L 187 ASN C 187 ASN ** K 98 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 = 0.4109 r_free = 0.4109 target = 0.175215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121198 restraints weight = 21243.037| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.00 r_work: 0.3302 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 15697 Z= 0.221 Angle : 0.693 13.030 21159 Z= 0.354 Chirality : 0.043 0.200 2349 Planarity : 0.005 0.063 2775 Dihedral : 4.920 24.801 2174 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.60 % Allowed : 18.87 % Favored : 76.54 % 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 are not related in a simple way. whole: 0.06 (0.21), residues: 1844 helix: 0.65 (0.16), residues: 1108 sheet: -0.98 (0.37), residues: 190 loop : -0.61 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 96 TYR 0.022 0.002 TYR A 49 PHE 0.031 0.002 PHE H 89 Details of bonding type rmsd covalent geometry : bond 0.00550 (15697) covalent geometry : angle 0.69332 (21159) hydrogen bonds : bond 0.03910 ( 817) hydrogen bonds : angle 4.74726 ( 2385) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 412 time to evaluate : 0.654 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: H 17 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7772 (t80) REVERT: H 39 ASP cc_start: 0.8866 (t70) cc_final: 0.8318 (t0) REVERT: H 86 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7689 (tt) REVERT: J 154 ASP cc_start: 0.8838 (t0) cc_final: 0.8540 (t0) REVERT: J 174 LYS cc_start: 0.8361 (mttt) cc_final: 0.8122 (mttt) REVERT: F 17 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.7045 (t80) REVERT: F 166 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8021 (mtmm) REVERT: F 169 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 166 LYS cc_start: 0.8173 (tppp) cc_final: 0.7845 (tttt) REVERT: D 39 ASP cc_start: 0.8706 (t70) cc_final: 0.8155 (t70) REVERT: L 29 SER cc_start: 0.8746 (t) cc_final: 0.8244 (p) REVERT: L 34 LEU cc_start: 0.8511 (mm) cc_final: 0.8136 (mm) REVERT: E 26 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8525 (tm-30) REVERT: E 39 ASP cc_start: 0.9097 (t70) cc_final: 0.8270 (t0) REVERT: E 50 GLN cc_start: 0.8243 (tp-100) cc_final: 0.8022 (tp-100) REVERT: E 138 LEU cc_start: 0.8431 (tp) cc_final: 0.8181 (tp) REVERT: E 164 MET cc_start: 0.8810 (tpp) cc_final: 0.8171 (ttm) REVERT: E 177 ASN cc_start: 0.8939 (t0) cc_final: 0.8709 (t0) REVERT: C 21 ASP cc_start: 0.7134 (t70) cc_final: 0.6748 (t0) REVERT: C 39 ASP cc_start: 0.8847 (t70) cc_final: 0.8442 (t70) REVERT: C 51 GLU cc_start: 0.8826 (tt0) cc_final: 0.8581 (tt0) REVERT: C 137 ILE cc_start: 0.7596 (mt) cc_final: 0.7303 (mp) REVERT: C 186 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6859 (mt0) REVERT: C 187 ASN cc_start: 0.7998 (m-40) cc_final: 0.7768 (m-40) REVERT: G 17 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.6620 (t80) REVERT: G 50 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8316 (tm-30) REVERT: G 133 MET cc_start: 0.7538 (pmm) cc_final: 0.7328 (pmm) REVERT: K 1 SER cc_start: 0.8102 (p) cc_final: 0.7780 (p) REVERT: K 25 MET cc_start: 0.5354 (mmt) cc_final: 0.4552 (ttp) REVERT: K 39 ASP cc_start: 0.8028 (t70) cc_final: 0.7544 (t0) REVERT: K 79 MET cc_start: 0.7836 (tpt) cc_final: 0.7459 (tpp) REVERT: K 166 LYS cc_start: 0.8486 (mppt) cc_final: 0.8132 (mppt) REVERT: K 173 ILE cc_start: 0.8747 (mt) cc_final: 0.8034 (tt) REVERT: K 185 MET cc_start: 0.7868 (mmm) cc_final: 0.7641 (mmm) REVERT: I 13 ASN cc_start: 0.8503 (t0) cc_final: 0.8192 (t0) REVERT: I 17 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6229 (t80) REVERT: I 26 GLN cc_start: 0.8330 (tp40) cc_final: 0.7986 (tp40) REVERT: I 39 ASP cc_start: 0.7764 (t0) cc_final: 0.7500 (t0) REVERT: I 51 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8472 (tm-30) REVERT: I 70 TYR cc_start: 0.8810 (m-10) cc_final: 0.8321 (m-10) REVERT: I 161 ASP cc_start: 0.7778 (t0) cc_final: 0.7439 (t0) outliers start: 77 outliers final: 48 residues processed: 455 average time/residue: 0.1205 time to fit residues: 83.8512 Evaluate side-chains 446 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 392 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 TYR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 77 PHE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 125 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 187 ASN K 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.177055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123555 restraints weight = 21223.444| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.99 r_work: 0.3334 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15697 Z= 0.175 Angle : 0.672 13.373 21159 Z= 0.342 Chirality : 0.043 0.206 2349 Planarity : 0.005 0.061 2775 Dihedral : 4.786 25.013 2174 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.12 % Allowed : 19.94 % Favored : 75.94 % 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 are not related in a simple way. whole: 0.17 (0.21), residues: 1844 helix: 0.68 (0.16), residues: 1119 sheet: -0.92 (0.37), residues: 190 loop : -0.43 (0.31), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 96 TYR 0.026 0.002 TYR A 49 PHE 0.035 0.002 PHE H 89 Details of bonding type rmsd covalent geometry : bond 0.00432 (15697) covalent geometry : angle 0.67176 (21159) hydrogen bonds : bond 0.03661 ( 817) hydrogen bonds : angle 4.65085 ( 2385) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 410 time to evaluate : 0.641 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: H 39 ASP cc_start: 0.8841 (t70) cc_final: 0.8300 (t70) REVERT: J 89 PHE cc_start: 0.9038 (t80) cc_final: 0.8697 (t80) REVERT: J 169 GLU cc_start: 0.8559 (tt0) cc_final: 0.8173 (pt0) REVERT: J 174 LYS cc_start: 0.8372 (mttt) cc_final: 0.7682 (mtpt) REVERT: F 17 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.7046 (t80) REVERT: F 44 MET cc_start: 0.8244 (ttm) cc_final: 0.7912 (ttp) REVERT: F 84 GLU cc_start: 0.7950 (tp30) cc_final: 0.7723 (tp30) REVERT: F 169 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7709 (tm-30) REVERT: B 166 LYS cc_start: 0.8159 (tppp) cc_final: 0.7840 (tttt) REVERT: D 39 ASP cc_start: 0.8666 (t70) cc_final: 0.8114 (t70) REVERT: L 29 SER cc_start: 0.8760 (t) cc_final: 0.8258 (p) REVERT: L 34 LEU cc_start: 0.8489 (mm) cc_final: 0.8105 (mm) REVERT: L 41 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: E 26 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8502 (tm-30) REVERT: E 39 ASP cc_start: 0.9064 (t70) cc_final: 0.8246 (t0) REVERT: E 50 GLN cc_start: 0.8231 (tp-100) cc_final: 0.8020 (tp-100) REVERT: E 138 LEU cc_start: 0.8416 (tp) cc_final: 0.8170 (tp) REVERT: E 152 GLU cc_start: 0.8843 (tt0) cc_final: 0.8315 (tt0) REVERT: E 164 MET cc_start: 0.8774 (tpp) cc_final: 0.8136 (ttm) REVERT: E 177 ASN cc_start: 0.8942 (t0) cc_final: 0.8694 (t0) REVERT: C 21 ASP cc_start: 0.7107 (t70) cc_final: 0.6727 (t0) REVERT: C 39 ASP cc_start: 0.8822 (t70) cc_final: 0.8325 (t70) REVERT: C 186 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6812 (mt0) REVERT: C 187 ASN cc_start: 0.8110 (m-40) cc_final: 0.7857 (m-40) REVERT: G 17 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6650 (t80) REVERT: G 50 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8261 (tm-30) REVERT: G 86 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8188 (tt) REVERT: K 1 SER cc_start: 0.8144 (p) cc_final: 0.7830 (p) REVERT: K 25 MET cc_start: 0.5253 (mmt) cc_final: 0.4461 (ttp) REVERT: K 39 ASP cc_start: 0.8016 (t70) cc_final: 0.7541 (t0) REVERT: K 52 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.6922 (pp) REVERT: K 162 GLU cc_start: 0.7799 (mp0) cc_final: 0.7489 (mm-30) REVERT: K 173 ILE cc_start: 0.8686 (mt) cc_final: 0.8117 (tt) REVERT: I 13 ASN cc_start: 0.8549 (t0) cc_final: 0.8255 (t0) REVERT: I 17 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6054 (t80) REVERT: I 21 ASP cc_start: 0.7487 (t70) cc_final: 0.6958 (t70) REVERT: I 26 GLN cc_start: 0.8387 (tp40) cc_final: 0.8063 (tp40) REVERT: I 39 ASP cc_start: 0.7725 (t0) cc_final: 0.7448 (t0) REVERT: I 51 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8458 (tm-30) REVERT: I 70 TYR cc_start: 0.8802 (m-10) cc_final: 0.8373 (m-10) REVERT: A 96 ARG cc_start: 0.6819 (mtt90) cc_final: 0.6158 (ttp80) REVERT: A 164 MET cc_start: 0.7915 (ttt) cc_final: 0.7588 (ttm) outliers start: 69 outliers final: 47 residues processed: 450 average time/residue: 0.1210 time to fit residues: 83.2296 Evaluate side-chains 444 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 390 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 77 PHE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 112 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 187 ASN K 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.177399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123599 restraints weight = 21408.471| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.02 r_work: 0.3332 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15697 Z= 0.180 Angle : 0.684 13.292 21159 Z= 0.348 Chirality : 0.043 0.203 2349 Planarity : 0.005 0.063 2775 Dihedral : 4.776 25.202 2174 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.30 % Allowed : 20.60 % Favored : 75.10 % 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 are not related in a simple way. whole: 0.18 (0.21), residues: 1844 helix: 0.69 (0.16), residues: 1119 sheet: -0.90 (0.37), residues: 190 loop : -0.45 (0.30), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 96 TYR 0.030 0.002 TYR A 49 PHE 0.037 0.002 PHE H 89 Details of bonding type rmsd covalent geometry : bond 0.00445 (15697) covalent geometry : angle 0.68402 (21159) hydrogen bonds : bond 0.03693 ( 817) hydrogen bonds : angle 4.65963 ( 2385) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 409 time to evaluate : 0.612 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: H 39 ASP cc_start: 0.8844 (t70) cc_final: 0.8319 (t70) REVERT: H 86 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7504 (tt) REVERT: J 169 GLU cc_start: 0.8555 (tt0) cc_final: 0.8188 (pt0) REVERT: J 174 LYS cc_start: 0.8388 (mttt) cc_final: 0.8166 (mttt) REVERT: F 17 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.7051 (t80) REVERT: F 44 MET cc_start: 0.8272 (ttm) cc_final: 0.7941 (ttp) REVERT: F 84 GLU cc_start: 0.7947 (tp30) cc_final: 0.7719 (tp30) REVERT: F 162 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7553 (tm-30) REVERT: F 169 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7698 (tm-30) REVERT: F 185 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8232 (mpp) REVERT: B 166 LYS cc_start: 0.8116 (tppp) cc_final: 0.7820 (tttt) REVERT: D 39 ASP cc_start: 0.8659 (t70) cc_final: 0.8119 (t70) REVERT: L 29 SER cc_start: 0.8742 (t) cc_final: 0.8235 (p) REVERT: L 34 LEU cc_start: 0.8472 (mm) cc_final: 0.8097 (mm) REVERT: L 41 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: L 152 GLU cc_start: 0.8377 (tt0) cc_final: 0.8079 (tt0) REVERT: E 26 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8549 (tm-30) REVERT: E 39 ASP cc_start: 0.9074 (t70) cc_final: 0.8265 (t0) REVERT: E 50 GLN cc_start: 0.8245 (tp-100) cc_final: 0.8032 (tp-100) REVERT: E 138 LEU cc_start: 0.8433 (tp) cc_final: 0.8174 (tp) REVERT: E 152 GLU cc_start: 0.8857 (tt0) cc_final: 0.8311 (tt0) REVERT: E 164 MET cc_start: 0.8778 (tpp) cc_final: 0.8144 (ttm) REVERT: E 177 ASN cc_start: 0.8933 (t0) cc_final: 0.8688 (t0) REVERT: C 21 ASP cc_start: 0.7111 (t70) cc_final: 0.6713 (t0) REVERT: C 39 ASP cc_start: 0.8813 (t70) cc_final: 0.8383 (t70) REVERT: C 51 GLU cc_start: 0.8826 (tt0) cc_final: 0.8614 (tt0) REVERT: C 186 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6776 (mt0) REVERT: C 187 ASN cc_start: 0.8118 (m-40) cc_final: 0.7817 (m110) REVERT: G 17 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.6335 (t80) REVERT: G 50 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8192 (tm-30) REVERT: G 86 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8110 (tt) REVERT: K 1 SER cc_start: 0.8122 (p) cc_final: 0.7812 (p) REVERT: K 25 MET cc_start: 0.5242 (mmt) cc_final: 0.4475 (ttp) REVERT: K 39 ASP cc_start: 0.7989 (t70) cc_final: 0.7509 (t0) REVERT: K 52 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.6986 (pp) REVERT: K 162 GLU cc_start: 0.7809 (mp0) cc_final: 0.7419 (mm-30) REVERT: K 166 LYS cc_start: 0.8478 (mppt) cc_final: 0.8154 (mppt) REVERT: K 173 ILE cc_start: 0.8685 (mt) cc_final: 0.8132 (tt) REVERT: I 13 ASN cc_start: 0.8544 (t0) cc_final: 0.8251 (t0) REVERT: I 17 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.5978 (t80) REVERT: I 21 ASP cc_start: 0.7490 (t70) cc_final: 0.6985 (t70) REVERT: I 26 GLN cc_start: 0.8489 (tp40) cc_final: 0.8192 (tp40) REVERT: I 39 ASP cc_start: 0.7720 (t0) cc_final: 0.7448 (t0) REVERT: I 51 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8424 (tm-30) REVERT: I 70 TYR cc_start: 0.8814 (m-10) cc_final: 0.8396 (m-10) REVERT: I 133 MET cc_start: 0.3877 (ptp) cc_final: 0.3662 (ptp) REVERT: I 169 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 96 ARG cc_start: 0.6678 (mtt90) cc_final: 0.6112 (ttp80) REVERT: A 164 MET cc_start: 0.7899 (ttt) cc_final: 0.7572 (ttm) outliers start: 72 outliers final: 46 residues processed: 447 average time/residue: 0.1194 time to fit residues: 82.1143 Evaluate side-chains 453 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 398 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 185 MET Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 187 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.180102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126957 restraints weight = 21252.244| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.03 r_work: 0.3378 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15697 Z= 0.145 Angle : 0.675 13.466 21159 Z= 0.340 Chirality : 0.043 0.229 2349 Planarity : 0.005 0.067 2775 Dihedral : 4.672 24.871 2174 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.52 % Allowed : 21.91 % Favored : 74.57 % 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 are not related in a simple way. whole: 0.31 (0.21), residues: 1844 helix: 0.78 (0.16), residues: 1117 sheet: -0.79 (0.37), residues: 190 loop : -0.39 (0.30), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 96 TYR 0.025 0.001 TYR A 49 PHE 0.048 0.002 PHE H 89 Details of bonding type rmsd covalent geometry : bond 0.00351 (15697) covalent geometry : angle 0.67474 (21159) hydrogen bonds : bond 0.03492 ( 817) hydrogen bonds : angle 4.61279 ( 2385) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 423 time to evaluate : 0.679 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: H 39 ASP cc_start: 0.8788 (t70) cc_final: 0.8244 (t70) REVERT: H 86 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7729 (tt) REVERT: J 89 PHE cc_start: 0.9111 (t80) cc_final: 0.8780 (t80) REVERT: J 169 GLU cc_start: 0.8538 (tt0) cc_final: 0.8176 (pt0) REVERT: J 174 LYS cc_start: 0.8436 (mttt) cc_final: 0.8213 (mttt) REVERT: F 17 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.7023 (t80) REVERT: F 44 MET cc_start: 0.8221 (ttm) cc_final: 0.7927 (ttp) REVERT: F 84 GLU cc_start: 0.7914 (tp30) cc_final: 0.7684 (tp30) REVERT: F 162 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7520 (tm-30) REVERT: F 169 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7670 (tm-30) REVERT: F 185 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8071 (mpp) REVERT: B 144 ILE cc_start: 0.7422 (mm) cc_final: 0.7217 (mm) REVERT: B 166 LYS cc_start: 0.8118 (tppp) cc_final: 0.7833 (tttt) REVERT: D 25 MET cc_start: 0.5472 (tpp) cc_final: 0.5245 (tpp) REVERT: D 39 ASP cc_start: 0.8593 (t70) cc_final: 0.8045 (t70) REVERT: L 29 SER cc_start: 0.8826 (t) cc_final: 0.8324 (p) REVERT: L 34 LEU cc_start: 0.8430 (mm) cc_final: 0.8213 (mm) REVERT: L 152 GLU cc_start: 0.8418 (tt0) cc_final: 0.8111 (tt0) REVERT: E 26 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8451 (tm-30) REVERT: E 39 ASP cc_start: 0.9048 (t70) cc_final: 0.8236 (t0) REVERT: E 50 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7957 (tp-100) REVERT: E 138 LEU cc_start: 0.8412 (tp) cc_final: 0.8149 (tp) REVERT: E 152 GLU cc_start: 0.8789 (tt0) cc_final: 0.8247 (tt0) REVERT: E 164 MET cc_start: 0.8745 (tpp) cc_final: 0.8056 (ttm) REVERT: E 177 ASN cc_start: 0.8963 (t0) cc_final: 0.8715 (t0) REVERT: C 21 ASP cc_start: 0.7114 (t70) cc_final: 0.6848 (t70) REVERT: C 39 ASP cc_start: 0.8754 (t70) cc_final: 0.7895 (t70) REVERT: C 186 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6770 (mp10) REVERT: C 187 ASN cc_start: 0.8134 (m-40) cc_final: 0.7879 (m-40) REVERT: G 50 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8175 (tm-30) REVERT: G 88 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7177 (mm-30) REVERT: G 91 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8228 (mp0) REVERT: G 162 GLU cc_start: 0.8394 (tp30) cc_final: 0.8139 (tp30) REVERT: G 170 ARG cc_start: 0.8514 (ttp-170) cc_final: 0.8309 (ttp80) REVERT: K 1 SER cc_start: 0.8142 (p) cc_final: 0.7849 (p) REVERT: K 25 MET cc_start: 0.5260 (mmt) cc_final: 0.4513 (ttp) REVERT: K 39 ASP cc_start: 0.7988 (t70) cc_final: 0.7523 (t0) REVERT: K 162 GLU cc_start: 0.7820 (mp0) cc_final: 0.7531 (mm-30) REVERT: K 173 ILE cc_start: 0.8660 (mt) cc_final: 0.8130 (tt) REVERT: I 13 ASN cc_start: 0.8576 (t0) cc_final: 0.8288 (t0) REVERT: I 17 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.5912 (t80) REVERT: I 21 ASP cc_start: 0.7488 (t70) cc_final: 0.7017 (t70) REVERT: I 26 GLN cc_start: 0.8449 (tp40) cc_final: 0.8162 (tp40) REVERT: I 39 ASP cc_start: 0.7599 (t0) cc_final: 0.7310 (t0) REVERT: I 51 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8410 (tm-30) REVERT: I 70 TYR cc_start: 0.8808 (m-10) cc_final: 0.8369 (m-10) REVERT: I 133 MET cc_start: 0.3920 (ptp) cc_final: 0.3657 (ptt) REVERT: I 162 GLU cc_start: 0.8357 (tp30) cc_final: 0.8014 (tp30) REVERT: I 169 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 96 ARG cc_start: 0.6736 (mtt90) cc_final: 0.6203 (ttp80) REVERT: A 164 MET cc_start: 0.7842 (ttt) cc_final: 0.7615 (ttm) outliers start: 59 outliers final: 40 residues processed: 456 average time/residue: 0.1191 time to fit residues: 82.8736 Evaluate side-chains 449 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 404 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 185 MET Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 142 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 137 optimal weight: 0.0470 chunk 63 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 187 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.176921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123431 restraints weight = 21409.030| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.01 r_work: 0.3329 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15697 Z= 0.202 Angle : 0.729 15.973 21159 Z= 0.368 Chirality : 0.044 0.209 2349 Planarity : 0.005 0.065 2775 Dihedral : 4.816 21.910 2174 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.40 % Allowed : 22.57 % Favored : 74.03 % 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 are not related in a simple way. whole: 0.22 (0.21), residues: 1844 helix: 0.71 (0.16), residues: 1113 sheet: -0.84 (0.37), residues: 190 loop : -0.42 (0.30), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 96 TYR 0.027 0.002 TYR A 49 PHE 0.024 0.002 PHE D 89 Details of bonding type rmsd covalent geometry : bond 0.00504 (15697) covalent geometry : angle 0.72852 (21159) hydrogen bonds : bond 0.03732 ( 817) hydrogen bonds : angle 4.77295 ( 2385) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 406 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 ASP cc_start: 0.8872 (t70) cc_final: 0.8349 (t70) REVERT: J 169 GLU cc_start: 0.8543 (tt0) cc_final: 0.8170 (pt0) REVERT: J 174 LYS cc_start: 0.8449 (mttt) cc_final: 0.8246 (mttt) REVERT: F 17 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.7098 (t80) REVERT: F 44 MET cc_start: 0.8325 (ttm) cc_final: 0.7997 (ttp) REVERT: F 84 GLU cc_start: 0.7987 (tp30) cc_final: 0.7742 (tp30) REVERT: F 162 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7555 (tm-30) REVERT: F 169 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7692 (tm-30) REVERT: F 185 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8239 (mpp) REVERT: B 144 ILE cc_start: 0.7380 (mm) cc_final: 0.7150 (mm) REVERT: B 148 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6755 (mm) REVERT: B 157 LEU cc_start: 0.8294 (tp) cc_final: 0.7922 (pp) REVERT: B 166 LYS cc_start: 0.8089 (tppp) cc_final: 0.7801 (tttt) REVERT: D 39 ASP cc_start: 0.8597 (t70) cc_final: 0.8077 (t70) REVERT: L 29 SER cc_start: 0.8790 (t) cc_final: 0.8288 (p) REVERT: L 34 LEU cc_start: 0.8467 (mm) cc_final: 0.8265 (mm) REVERT: L 41 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: L 152 GLU cc_start: 0.8392 (tt0) cc_final: 0.8106 (tt0) REVERT: E 26 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8581 (tm-30) REVERT: E 39 ASP cc_start: 0.9093 (t70) cc_final: 0.8299 (t0) REVERT: E 152 GLU cc_start: 0.8846 (tt0) cc_final: 0.8218 (tt0) REVERT: E 164 MET cc_start: 0.8774 (tpp) cc_final: 0.8174 (ttm) REVERT: E 177 ASN cc_start: 0.8946 (t0) cc_final: 0.8714 (t0) REVERT: C 21 ASP cc_start: 0.7136 (t70) cc_final: 0.6699 (t0) REVERT: C 39 ASP cc_start: 0.8842 (t70) cc_final: 0.8397 (t70) REVERT: C 186 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6841 (mt0) REVERT: C 187 ASN cc_start: 0.8140 (m-40) cc_final: 0.7859 (m110) REVERT: G 50 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8144 (tm-30) REVERT: G 91 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8291 (mp0) REVERT: G 185 MET cc_start: 0.8357 (mtm) cc_final: 0.8074 (mtt) REVERT: K 1 SER cc_start: 0.8136 (p) cc_final: 0.7836 (p) REVERT: K 25 MET cc_start: 0.5250 (mmt) cc_final: 0.4482 (ttp) REVERT: K 39 ASP cc_start: 0.8028 (t70) cc_final: 0.7556 (t0) REVERT: K 98 GLN cc_start: 0.5865 (tm-30) cc_final: 0.5187 (mp10) REVERT: K 173 ILE cc_start: 0.8682 (mt) cc_final: 0.8096 (tt) REVERT: I 13 ASN cc_start: 0.8563 (t0) cc_final: 0.8267 (t0) REVERT: I 17 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6082 (t80) REVERT: I 21 ASP cc_start: 0.7597 (t70) cc_final: 0.7105 (t70) REVERT: I 26 GLN cc_start: 0.8584 (tp40) cc_final: 0.8323 (tp40) REVERT: I 39 ASP cc_start: 0.7682 (t0) cc_final: 0.7399 (t0) REVERT: I 51 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8416 (tm-30) REVERT: I 70 TYR cc_start: 0.8859 (m-10) cc_final: 0.8408 (m-10) REVERT: I 133 MET cc_start: 0.3928 (ptp) cc_final: 0.3707 (ptp) REVERT: I 187 ASN cc_start: 0.8822 (m-40) cc_final: 0.8338 (m110) REVERT: A 96 ARG cc_start: 0.6700 (mtt90) cc_final: 0.6146 (ttp80) REVERT: A 164 MET cc_start: 0.7902 (ttt) cc_final: 0.7573 (ttm) outliers start: 57 outliers final: 43 residues processed: 435 average time/residue: 0.1214 time to fit residues: 81.1831 Evaluate side-chains 451 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 402 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain J residue 13 ASN Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 90 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 185 MET Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 25 MET Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 187 ASN Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 TYR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 17 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 133 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 131 optimal weight: 9.9990 chunk 53 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 chunk 141 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 187 ASN E 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.182018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129424 restraints weight = 21191.421| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.03 r_work: 0.3404 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15697 Z= 0.139 Angle : 0.689 16.373 21159 Z= 0.348 Chirality : 0.043 0.204 2349 Planarity : 0.005 0.065 2775 Dihedral : 4.625 20.822 2174 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.69 % Allowed : 23.16 % Favored : 74.15 % 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 are not related in a simple way. whole: 0.33 (0.21), residues: 1844 helix: 0.80 (0.17), residues: 1113 sheet: -0.76 (0.37), residues: 190 loop : -0.37 (0.30), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 96 TYR 0.022 0.001 TYR A 49 PHE 0.038 0.001 PHE C 89 Details of bonding type rmsd covalent geometry : bond 0.00329 (15697) covalent geometry : angle 0.68921 (21159) hydrogen bonds : bond 0.03398 ( 817) hydrogen bonds : angle 4.64493 ( 2385) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4301.54 seconds wall clock time: 74 minutes 25.86 seconds (4465.86 seconds total)