Starting phenix.real_space_refine on Mon May 4 08:20:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zbi_73989/05_2026/9zbi_73989.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zbi_73989/05_2026/9zbi_73989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zbi_73989/05_2026/9zbi_73989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zbi_73989/05_2026/9zbi_73989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zbi_73989/05_2026/9zbi_73989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zbi_73989/05_2026/9zbi_73989.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 48 5.16 5 C 12234 2.51 5 N 3366 2.21 5 O 3675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19323 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2701 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2701 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2701 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2701 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2701 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "F" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2701 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "G" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1039 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain: "H" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1039 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain: "I" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1039 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 133} Time building chain proxies: 4.24, per 1000 atoms: 0.22 Number of scatterers: 19323 At special positions: 0 Unit cell: (181.146, 216.558, 114.408, 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 48 16.00 O 3675 8.00 N 3366 7.00 C 12234 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: 1.61 Conformation dependent library (CDL) restraints added in 813.8 milliseconds 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4470 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 35 sheets defined 27.6% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.908A pdb=" N ILE A 98 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 142 removed outlier: 3.680A pdb=" N VAL A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.962A pdb=" N LYS A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.526A pdb=" N ILE A 337 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 Processing helix chain 'B' and resid 111 through 142 removed outlier: 3.657A pdb=" N VAL B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'C' and resid 111 through 142 removed outlier: 3.675A pdb=" N VAL C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 176 through 191 removed outlier: 4.141A pdb=" N LYS C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 214 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 295 through 299 removed outlier: 3.597A pdb=" N ASP C 298 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 299 " --> pdb=" O PHE C 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 295 through 299' Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.568A pdb=" N ILE C 337 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 36 Processing helix chain 'D' and resid 111 through 142 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 333 through 337 removed outlier: 3.724A pdb=" N ILE D 337 " --> pdb=" O PRO D 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 36 Processing helix chain 'E' and resid 94 through 98 Processing helix chain 'E' and resid 111 through 142 removed outlier: 3.675A pdb=" N VAL E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 176 through 191 removed outlier: 4.182A pdb=" N LYS E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 216 through 227 Processing helix chain 'E' and resid 333 through 337 removed outlier: 3.504A pdb=" N ILE E 337 " --> pdb=" O PRO E 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 36 Processing helix chain 'F' and resid 111 through 142 removed outlier: 3.593A pdb=" N VAL F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 176 through 191 removed outlier: 3.863A pdb=" N LYS F 180 " --> pdb=" O ASP F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 Processing helix chain 'F' and resid 216 through 227 Processing helix chain 'F' and resid 295 through 299 removed outlier: 3.998A pdb=" N LEU F 299 " --> pdb=" O PHE F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 removed outlier: 3.742A pdb=" N ILE F 337 " --> pdb=" O PRO F 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 16 removed outlier: 4.190A pdb=" N TRP G 16 " --> pdb=" O ARG G 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 12 through 16' Processing helix chain 'G' and resid 24 through 28 Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 73 through 79 removed outlier: 3.569A pdb=" N MET G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 117 Processing helix chain 'H' and resid 12 through 16 removed outlier: 4.193A pdb=" N TRP H 16 " --> pdb=" O ARG H 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 12 through 16' Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 59 through 63 removed outlier: 3.618A pdb=" N ALA H 63 " --> pdb=" O ILE H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 79 removed outlier: 3.918A pdb=" N MET H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 118 removed outlier: 3.580A pdb=" N LYS H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 16 removed outlier: 4.398A pdb=" N TRP I 16 " --> pdb=" O ARG I 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 12 through 16' Processing helix chain 'I' and resid 24 through 28 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 59 through 63 removed outlier: 4.156A pdb=" N ALA I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 79 Processing helix chain 'I' and resid 104 through 117 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.640A pdb=" N ASP A 17 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N GLU B 51 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.640A pdb=" N ASP A 17 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N GLU B 51 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 42 removed outlier: 3.636A pdb=" N THR A 39 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 82 removed outlier: 3.566A pdb=" N ARG A 76 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 76 through 82 removed outlier: 3.566A pdb=" N ARG A 76 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N LEU F 22 " --> pdb=" O GLN A 49 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU A 51 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE F 24 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 53 " --> pdb=" O ILE F 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 62 through 63 removed outlier: 4.399A pdb=" N HIS F 86 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 87 through 93 Processing sheet with id=AA8, first strand: chain 'A' and resid 165 through 167 removed outlier: 6.976A pdb=" N PHE A 201 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE A 257 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 203 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG A 247 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 17 through 18 removed outlier: 6.076A pdb=" N ASP B 17 " --> pdb=" O GLN C 49 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N GLU C 51 " --> pdb=" O ASP B 17 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 18 removed outlier: 6.076A pdb=" N ASP B 17 " --> pdb=" O GLN C 49 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N GLU C 51 " --> pdb=" O ASP B 17 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 39 through 42 removed outlier: 3.659A pdb=" N THR B 39 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 93 Processing sheet with id=AB4, first strand: chain 'B' and resid 164 through 167 removed outlier: 7.013A pdb=" N PHE B 201 " --> pdb=" O HIS B 255 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE B 257 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA B 203 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG B 247 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 22 through 24 Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 42 removed outlier: 6.218A pdb=" N THR C 39 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N PHE C 290 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLU C 41 " --> pdb=" O PHE C 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 307 through 312 removed outlier: 4.326A pdb=" N HIS C 86 " --> pdb=" O ALA D 63 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.850A pdb=" N PHE C 201 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE C 257 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA C 203 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 17 through 18 removed outlier: 5.870A pdb=" N ASP D 17 " --> pdb=" O GLN E 49 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU E 51 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 17 through 18 removed outlier: 5.870A pdb=" N ASP D 17 " --> pdb=" O GLN E 49 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU E 51 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.174A pdb=" N THR D 39 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE D 290 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLU D 41 " --> pdb=" O PHE D 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 307 through 312 removed outlier: 4.021A pdb=" N HIS D 86 " --> pdb=" O ALA E 63 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 165 through 167 removed outlier: 4.213A pdb=" N ARG D 247 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 17 through 18 removed outlier: 6.093A pdb=" N ASP E 17 " --> pdb=" O GLN F 49 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU F 51 " --> pdb=" O ASP E 17 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 17 through 18 removed outlier: 6.093A pdb=" N ASP E 17 " --> pdb=" O GLN F 49 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU F 51 " --> pdb=" O ASP E 17 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 39 through 42 removed outlier: 3.791A pdb=" N THR E 39 " --> pdb=" O PHE E 286 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 290 " --> pdb=" O GLU E 41 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 87 through 93 Processing sheet with id=AC9, first strand: chain 'E' and resid 165 through 167 removed outlier: 6.864A pdb=" N PHE E 201 " --> pdb=" O HIS E 255 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE E 257 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA E 203 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 39 through 42 removed outlier: 3.669A pdb=" N THR F 39 " --> pdb=" O PHE F 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 165 through 167 removed outlier: 6.865A pdb=" N PHE F 201 " --> pdb=" O HIS F 255 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE F 257 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA F 203 " --> pdb=" O ILE F 257 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 17 through 20 removed outlier: 6.680A pdb=" N LEU G 17 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY G 93 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA G 90 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL G 123 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE G 92 " --> pdb=" O VAL G 123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 31 through 35 removed outlier: 3.529A pdb=" N ILE G 66 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU G 48 " --> pdb=" O THR G 64 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 17 through 20 removed outlier: 6.915A pdb=" N LEU H 17 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY H 93 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA H 90 " --> pdb=" O PHE H 121 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL H 123 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE H 92 " --> pdb=" O VAL H 123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 31 through 35 Processing sheet with id=AD7, first strand: chain 'I' and resid 17 through 20 removed outlier: 6.732A pdb=" N LEU I 17 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY I 93 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA I 90 " --> pdb=" O PHE I 121 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL I 123 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE I 92 " --> pdb=" O VAL I 123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 31 through 35 709 hydrogen bonds defined for protein. 1938 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: 2.83 Time building geometry restraints manager: 2.11 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: 6509 1.34 - 1.46: 3398 1.46 - 1.57: 9749 1.57 - 1.69: 0 1.69 - 1.80: 90 Bond restraints: 19746 Sorted by residual: bond pdb=" C ASP F 263 " pdb=" N PRO F 264 " ideal model delta sigma weight residual 1.334 1.360 -0.027 2.34e-02 1.83e+03 1.28e+00 bond pdb=" C ILE E 84 " pdb=" N PRO E 85 " ideal model delta sigma weight residual 1.334 1.358 -0.025 2.34e-02 1.83e+03 1.10e+00 bond pdb=" CB ASP C 90 " pdb=" CG ASP C 90 " ideal model delta sigma weight residual 1.516 1.492 0.024 2.50e-02 1.60e+03 9.11e-01 bond pdb=" CA LEU F 170 " pdb=" C LEU F 170 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.80e-02 3.09e+03 8.13e-01 bond pdb=" CA ILE B 278 " pdb=" CB ILE B 278 " ideal model delta sigma weight residual 1.537 1.549 -0.011 1.29e-02 6.01e+03 7.88e-01 ... (remaining 19741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 25895 1.25 - 2.50: 723 2.50 - 3.75: 111 3.75 - 5.00: 15 5.00 - 6.25: 10 Bond angle restraints: 26754 Sorted by residual: angle pdb=" C GLN F 75 " pdb=" N ARG F 76 " pdb=" CA ARG F 76 " ideal model delta sigma weight residual 123.01 118.91 4.10 1.78e+00 3.16e-01 5.31e+00 angle pdb=" C GLN E 75 " pdb=" N ARG E 76 " pdb=" CA ARG E 76 " ideal model delta sigma weight residual 122.11 118.57 3.54 1.59e+00 3.96e-01 4.96e+00 angle pdb=" N ASP A 284 " pdb=" CA ASP A 284 " pdb=" CB ASP A 284 " ideal model delta sigma weight residual 113.65 110.39 3.26 1.47e+00 4.63e-01 4.93e+00 angle pdb=" N TYR D 14 " pdb=" CA TYR D 14 " pdb=" CB TYR D 14 " ideal model delta sigma weight residual 110.49 114.03 -3.54 1.69e+00 3.50e-01 4.39e+00 angle pdb=" N TYR C 57 " pdb=" CA TYR C 57 " pdb=" C TYR C 57 " ideal model delta sigma weight residual 109.18 112.07 -2.89 1.42e+00 4.96e-01 4.15e+00 ... (remaining 26749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 10589 16.44 - 32.88: 831 32.88 - 49.32: 192 49.32 - 65.76: 73 65.76 - 82.20: 6 Dihedral angle restraints: 11691 sinusoidal: 4722 harmonic: 6969 Sorted by residual: dihedral pdb=" CA TYR C 265 " pdb=" C TYR C 265 " pdb=" N GLY C 266 " pdb=" CA GLY C 266 " ideal model delta harmonic sigma weight residual -180.00 -158.50 -21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LYS B 61 " pdb=" C LYS B 61 " pdb=" N ASP B 62 " pdb=" CA ASP B 62 " ideal model delta harmonic sigma weight residual 180.00 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA TYR B 265 " pdb=" C TYR B 265 " pdb=" N GLY B 266 " pdb=" CA GLY B 266 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 11688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1722 0.030 - 0.060: 727 0.060 - 0.090: 250 0.090 - 0.120: 153 0.120 - 0.151: 46 Chirality restraints: 2898 Sorted by residual: chirality pdb=" CA ILE F 321 " pdb=" N ILE F 321 " pdb=" C ILE F 321 " pdb=" CB ILE F 321 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE D 321 " pdb=" N ILE D 321 " pdb=" C ILE D 321 " pdb=" CB ILE D 321 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ILE B 321 " pdb=" N ILE B 321 " pdb=" C ILE B 321 " pdb=" CB ILE B 321 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 2895 not shown) Planarity restraints: 3534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 84 " 0.029 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 85 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 84 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO F 85 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 85 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 85 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 263 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO B 264 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 264 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 264 " -0.022 5.00e-02 4.00e+02 ... (remaining 3531 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 10146 3.00 - 3.48: 17475 3.48 - 3.95: 28660 3.95 - 4.43: 33671 4.43 - 4.90: 56760 Nonbonded interactions: 146712 Sorted by model distance: nonbonded pdb=" N THR F 44 " pdb=" OG1 THR F 44 " model vdw 2.526 2.496 nonbonded pdb=" O HIS A 86 " pdb=" O ASP B 62 " model vdw 2.539 3.040 nonbonded pdb=" N THR B 162 " pdb=" OG1 THR B 162 " model vdw 2.561 2.496 nonbonded pdb=" N VAL C 177 " pdb=" CG2 VAL C 177 " model vdw 2.561 2.832 nonbonded pdb=" C THR F 141 " pdb=" OG1 THR F 141 " model vdw 2.567 2.616 ... (remaining 146707 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.580 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.004 0.030 19746 Z= 0.166 Angle : 0.521 6.251 26754 Z= 0.287 Chirality : 0.044 0.151 2898 Planarity : 0.004 0.045 3534 Dihedral : 13.307 82.205 7221 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 5.30 % Allowed : 7.78 % Favored : 86.92 % 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: -0.79 (0.16), residues: 2391 helix: 1.61 (0.22), residues: 563 sheet: 0.35 (0.24), residues: 439 loop : -1.84 (0.14), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.017 0.001 TYR D 92 PHE 0.016 0.002 PHE F 13 TRP 0.012 0.002 TRP E 155 HIS 0.005 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00372 (19746) covalent geometry : angle 0.52124 (26754) hydrogen bonds : bond 0.13370 ( 702) hydrogen bonds : angle 6.35786 ( 1938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 456 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8453 (p0) REVERT: A 183 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 188 MET cc_start: 0.8670 (mmt) cc_final: 0.8354 (mmt) REVERT: A 200 ASP cc_start: 0.7775 (m-30) cc_final: 0.7559 (p0) REVERT: A 219 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7775 (mm) REVERT: A 265 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.6476 (m-80) REVERT: A 281 ASP cc_start: 0.6146 (t70) cc_final: 0.5945 (p0) REVERT: A 316 ARG cc_start: 0.7530 (ttm-80) cc_final: 0.6569 (tpt170) REVERT: B 15 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8171 (mm) REVERT: B 74 ASP cc_start: 0.8032 (m-30) cc_final: 0.7639 (m-30) REVERT: B 76 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.4369 (ppt-90) REVERT: B 101 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8523 (mptt) REVERT: B 102 ARG cc_start: 0.6612 (mmt180) cc_final: 0.4307 (ttt90) REVERT: B 143 LYS cc_start: 0.8851 (mttm) cc_final: 0.8388 (mttt) REVERT: B 157 ASP cc_start: 0.8472 (t70) cc_final: 0.8097 (t70) REVERT: B 159 MET cc_start: 0.8245 (mmt) cc_final: 0.8042 (mmm) REVERT: B 265 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: B 312 MET cc_start: 0.8638 (ttp) cc_final: 0.8010 (ttp) REVERT: B 316 ARG cc_start: 0.8187 (mtt-85) cc_final: 0.7911 (mtm180) REVERT: C 27 ASN cc_start: 0.8246 (m-40) cc_final: 0.7945 (m110) REVERT: C 101 LYS cc_start: 0.8439 (mmtt) cc_final: 0.7132 (ttpt) REVERT: C 102 ARG cc_start: 0.6404 (mmt180) cc_final: 0.4128 (ptp-170) REVERT: C 181 THR cc_start: 0.8888 (m) cc_final: 0.8389 (p) REVERT: C 294 SER cc_start: 0.8747 (m) cc_final: 0.8489 (t) REVERT: C 298 ASP cc_start: 0.8588 (m-30) cc_final: 0.8091 (m-30) REVERT: C 304 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8663 (mtpt) REVERT: C 310 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: C 311 ARG cc_start: 0.7669 (mtm180) cc_final: 0.7255 (ttm-80) REVERT: D 14 TYR cc_start: 0.4437 (t80) cc_final: 0.3310 (t80) REVERT: D 17 ASP cc_start: 0.7479 (t0) cc_final: 0.7139 (t0) REVERT: D 18 GLN cc_start: 0.8052 (tt0) cc_final: 0.7694 (mt0) REVERT: D 76 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.4795 (ptt180) REVERT: D 77 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7178 (ppt170) REVERT: D 97 ASP cc_start: 0.7408 (m-30) cc_final: 0.7085 (m-30) REVERT: D 102 ARG cc_start: 0.5769 (mmt180) cc_final: 0.3405 (ptt180) REVERT: D 116 ARG cc_start: 0.8002 (mtp85) cc_final: 0.7671 (mtp-110) REVERT: D 164 LYS cc_start: 0.7814 (tptt) cc_final: 0.7365 (tptm) REVERT: D 183 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7521 (tp30) REVERT: D 192 SER cc_start: 0.8721 (p) cc_final: 0.8342 (t) REVERT: D 317 ARG cc_start: 0.4886 (OUTLIER) cc_final: 0.4630 (ttm-80) REVERT: D 336 MET cc_start: 0.8930 (mmm) cc_final: 0.8692 (mmm) REVERT: E 12 GLN cc_start: 0.3513 (pm20) cc_final: 0.2433 (pm20) REVERT: E 13 PHE cc_start: 0.5361 (OUTLIER) cc_final: 0.5026 (m-80) REVERT: E 102 ARG cc_start: 0.6035 (mmt180) cc_final: 0.4519 (ttt90) REVERT: E 107 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6806 (m-30) REVERT: E 151 ILE cc_start: 0.9176 (pt) cc_final: 0.8706 (tt) REVERT: E 156 TYR cc_start: 0.8636 (m-80) cc_final: 0.8203 (m-80) REVERT: E 159 MET cc_start: 0.8803 (mmt) cc_final: 0.8292 (mmp) REVERT: E 284 ASP cc_start: 0.6654 (OUTLIER) cc_final: 0.6416 (p0) REVERT: E 297 ASP cc_start: 0.7631 (m-30) cc_final: 0.7425 (m-30) REVERT: E 311 ARG cc_start: 0.7664 (mtm180) cc_final: 0.7400 (mtm-85) REVERT: E 316 ARG cc_start: 0.7144 (ttm-80) cc_final: 0.5298 (tmt170) REVERT: E 322 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: E 336 MET cc_start: 0.8806 (mmm) cc_final: 0.8382 (mmm) REVERT: F 49 GLN cc_start: 0.8233 (mt0) cc_final: 0.7798 (mt0) REVERT: F 76 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8386 (mtt180) REVERT: F 102 ARG cc_start: 0.6461 (mmt180) cc_final: 0.3931 (pmm-80) REVERT: F 143 LYS cc_start: 0.8948 (mttt) cc_final: 0.8724 (mttp) REVERT: F 157 ASP cc_start: 0.8722 (t70) cc_final: 0.8312 (p0) REVERT: F 172 ASN cc_start: 0.7688 (p0) cc_final: 0.7351 (p0) REVERT: F 188 MET cc_start: 0.8860 (mmt) cc_final: 0.8653 (mmm) REVERT: F 194 ASP cc_start: 0.7655 (p0) cc_final: 0.7220 (p0) REVERT: F 196 LEU cc_start: 0.8535 (mt) cc_final: 0.7975 (mp) REVERT: F 224 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8178 (mtmm) REVERT: G 36 VAL cc_start: 0.7828 (p) cc_final: 0.7594 (t) REVERT: G 62 ASP cc_start: 0.7566 (t0) cc_final: 0.7256 (t0) REVERT: G 102 ASP cc_start: 0.7549 (p0) cc_final: 0.6998 (p0) REVERT: G 104 ASP cc_start: 0.7436 (m-30) cc_final: 0.7214 (m-30) REVERT: H 42 LYS cc_start: 0.8335 (mtpp) cc_final: 0.8132 (mtmt) REVERT: H 60 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7603 (mm) REVERT: H 79 MET cc_start: 0.8457 (mmt) cc_final: 0.8064 (mmm) REVERT: H 105 ASP cc_start: 0.7287 (m-30) cc_final: 0.6887 (m-30) REVERT: I 42 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8493 (mttm) REVERT: I 44 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8734 (t) outliers start: 107 outliers final: 44 residues processed: 528 average time/residue: 0.6505 time to fit residues: 382.2090 Evaluate side-chains 378 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 317 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 317 ARG Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 12 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 47 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 30.0000 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN B 191 ASN B 216 HIS D 326 ASN I 132 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112506 restraints weight = 33283.650| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.85 r_work: 0.3288 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19746 Z= 0.163 Angle : 0.530 5.972 26754 Z= 0.288 Chirality : 0.045 0.156 2898 Planarity : 0.004 0.060 3534 Dihedral : 8.078 76.802 2802 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 7.58 % Allowed : 14.41 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.16), residues: 2391 helix: 1.75 (0.22), residues: 573 sheet: 0.16 (0.24), residues: 453 loop : -1.84 (0.14), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 125 TYR 0.017 0.001 TYR D 92 PHE 0.033 0.002 PHE D 13 TRP 0.014 0.002 TRP B 155 HIS 0.005 0.001 HIS D 69 Details of bonding type rmsd covalent geometry : bond 0.00370 (19746) covalent geometry : angle 0.52993 (26754) hydrogen bonds : bond 0.05261 ( 702) hydrogen bonds : angle 5.40014 ( 1938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 336 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8436 (p0) REVERT: A 22 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7840 (mp) REVERT: A 47 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8788 (t) REVERT: A 77 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.4919 (ppt-90) REVERT: A 188 MET cc_start: 0.8672 (mmt) cc_final: 0.8389 (mmt) REVERT: A 200 ASP cc_start: 0.7681 (m-30) cc_final: 0.7387 (p0) REVERT: A 219 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7684 (mm) REVERT: A 281 ASP cc_start: 0.6172 (t70) cc_final: 0.5919 (p0) REVERT: A 316 ARG cc_start: 0.7415 (ttm-80) cc_final: 0.6589 (tpt170) REVERT: A 317 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.5538 (ttt180) REVERT: B 15 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8173 (mm) REVERT: B 74 ASP cc_start: 0.8070 (m-30) cc_final: 0.7649 (m-30) REVERT: B 76 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.4449 (ppt-90) REVERT: B 79 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8041 (mt) REVERT: B 96 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8448 (mt-10) REVERT: B 101 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8446 (mptt) REVERT: B 102 ARG cc_start: 0.6682 (mmt180) cc_final: 0.4331 (ttt90) REVERT: B 143 LYS cc_start: 0.8845 (mttm) cc_final: 0.8358 (mttt) REVERT: B 157 ASP cc_start: 0.8335 (t70) cc_final: 0.7992 (t70) REVERT: B 223 TYR cc_start: 0.8502 (m-80) cc_final: 0.8073 (m-80) REVERT: B 265 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.6827 (m-80) REVERT: B 312 MET cc_start: 0.8491 (ttp) cc_final: 0.7942 (ttp) REVERT: B 316 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7882 (mtm180) REVERT: C 27 ASN cc_start: 0.8229 (m-40) cc_final: 0.7935 (m110) REVERT: C 101 LYS cc_start: 0.8445 (mmtt) cc_final: 0.7151 (ttpt) REVERT: C 102 ARG cc_start: 0.6338 (mmt180) cc_final: 0.4106 (ptp-170) REVERT: C 181 THR cc_start: 0.8878 (m) cc_final: 0.8340 (p) REVERT: C 221 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: C 294 SER cc_start: 0.8732 (m) cc_final: 0.8448 (t) REVERT: C 298 ASP cc_start: 0.8537 (m-30) cc_final: 0.8186 (m-30) REVERT: C 304 LYS cc_start: 0.8906 (mtmm) cc_final: 0.8668 (mtpt) REVERT: C 311 ARG cc_start: 0.7696 (mtm180) cc_final: 0.7333 (ttm-80) REVERT: C 316 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.5892 (ppt170) REVERT: C 322 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7000 (mt-10) REVERT: C 326 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8172 (m110) REVERT: D 14 TYR cc_start: 0.4544 (t80) cc_final: 0.3429 (t80) REVERT: D 17 ASP cc_start: 0.7615 (t0) cc_final: 0.7219 (t0) REVERT: D 76 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.4829 (ptt180) REVERT: D 77 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7148 (ppt170) REVERT: D 91 ASP cc_start: 0.7589 (t0) cc_final: 0.7343 (t0) REVERT: D 97 ASP cc_start: 0.7480 (m-30) cc_final: 0.7250 (m-30) REVERT: D 102 ARG cc_start: 0.5808 (mmt180) cc_final: 0.3449 (ptt180) REVERT: D 116 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7758 (mtp-110) REVERT: D 164 LYS cc_start: 0.7854 (tptt) cc_final: 0.7422 (tptm) REVERT: D 183 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7624 (tp30) REVERT: D 192 SER cc_start: 0.8721 (p) cc_final: 0.8354 (t) REVERT: D 235 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7830 (tp30) REVERT: D 305 GLU cc_start: 0.7701 (mp0) cc_final: 0.7488 (mt-10) REVERT: D 312 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7619 (tpp) REVERT: D 317 ARG cc_start: 0.4411 (OUTLIER) cc_final: 0.4105 (ttm-80) REVERT: E 12 GLN cc_start: 0.3719 (pm20) cc_final: 0.2619 (pm20) REVERT: E 13 PHE cc_start: 0.5329 (OUTLIER) cc_final: 0.5049 (m-80) REVERT: E 71 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7532 (t) REVERT: E 102 ARG cc_start: 0.6022 (mmt180) cc_final: 0.3583 (mpp80) REVERT: E 151 ILE cc_start: 0.9185 (pt) cc_final: 0.8625 (tt) REVERT: E 156 TYR cc_start: 0.8561 (m-80) cc_final: 0.8110 (m-80) REVERT: E 159 MET cc_start: 0.8789 (mmt) cc_final: 0.8362 (mmp) REVERT: E 178 MET cc_start: 0.7905 (mmt) cc_final: 0.7585 (mmm) REVERT: E 235 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: E 250 TYR cc_start: 0.7968 (m-80) cc_final: 0.7334 (m-80) REVERT: E 284 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6400 (p0) REVERT: E 297 ASP cc_start: 0.7580 (m-30) cc_final: 0.7372 (m-30) REVERT: E 311 ARG cc_start: 0.7712 (mtm180) cc_final: 0.7409 (mtm-85) REVERT: E 316 ARG cc_start: 0.7064 (ttm-80) cc_final: 0.5254 (tpt90) REVERT: E 322 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: E 336 MET cc_start: 0.8963 (mmm) cc_final: 0.8567 (mmt) REVERT: F 49 GLN cc_start: 0.8238 (mt0) cc_final: 0.7805 (mt0) REVERT: F 76 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8434 (mtt180) REVERT: F 96 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: F 102 ARG cc_start: 0.6216 (mmt180) cc_final: 0.3638 (pmm-80) REVERT: F 143 LYS cc_start: 0.8941 (mttt) cc_final: 0.8727 (mttp) REVERT: F 157 ASP cc_start: 0.8722 (t70) cc_final: 0.8322 (p0) REVERT: F 172 ASN cc_start: 0.7593 (p0) cc_final: 0.7356 (p0) REVERT: F 176 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7634 (p0) REVERT: F 194 ASP cc_start: 0.7593 (p0) cc_final: 0.7318 (p0) REVERT: F 196 LEU cc_start: 0.8541 (mt) cc_final: 0.7995 (mp) REVERT: F 224 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8209 (mtmm) REVERT: F 243 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: F 281 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7153 (t0) REVERT: F 312 MET cc_start: 0.8223 (ttt) cc_final: 0.7974 (ttt) REVERT: G 36 VAL cc_start: 0.7902 (p) cc_final: 0.7571 (t) REVERT: G 62 ASP cc_start: 0.7410 (t0) cc_final: 0.7027 (t0) REVERT: H 42 LYS cc_start: 0.8400 (mtpp) cc_final: 0.8060 (mtmt) REVERT: H 60 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7741 (mm) REVERT: H 79 MET cc_start: 0.8476 (mmt) cc_final: 0.8088 (mmm) REVERT: I 44 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8774 (t) REVERT: I 57 LYS cc_start: 0.8037 (tmtm) cc_final: 0.7597 (tttt) REVERT: I 60 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8690 (tp) outliers start: 153 outliers final: 80 residues processed: 445 average time/residue: 0.6531 time to fit residues: 323.5688 Evaluate side-chains 413 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 302 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 317 ARG Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 12 GLN Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 60 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 173 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 255 HIS D 34 ASN D 326 ASN E 189 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110513 restraints weight = 33708.776| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.86 r_work: 0.3250 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19746 Z= 0.211 Angle : 0.575 6.572 26754 Z= 0.313 Chirality : 0.046 0.154 2898 Planarity : 0.005 0.061 3534 Dihedral : 8.158 79.997 2791 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.19 % Rotamer: Outliers : 8.17 % Allowed : 15.90 % Favored : 75.93 % 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: -0.92 (0.16), residues: 2391 helix: 1.56 (0.22), residues: 576 sheet: 0.11 (0.24), residues: 448 loop : -1.94 (0.14), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 125 TYR 0.018 0.002 TYR D 92 PHE 0.018 0.002 PHE C 87 TRP 0.016 0.002 TRP B 155 HIS 0.006 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00495 (19746) covalent geometry : angle 0.57500 (26754) hydrogen bonds : bond 0.05779 ( 702) hydrogen bonds : angle 5.42315 ( 1938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 308 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8505 (p0) REVERT: A 22 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7799 (mp) REVERT: A 47 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8790 (t) REVERT: A 77 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.5082 (ppt-90) REVERT: A 188 MET cc_start: 0.8680 (mmt) cc_final: 0.8325 (mmt) REVERT: A 200 ASP cc_start: 0.7708 (m-30) cc_final: 0.7348 (p0) REVERT: A 219 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7683 (mm) REVERT: A 265 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.6620 (m-80) REVERT: A 281 ASP cc_start: 0.6188 (t70) cc_final: 0.5970 (p0) REVERT: A 316 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.6580 (tpt170) REVERT: A 317 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.5622 (ttt180) REVERT: B 15 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8155 (mm) REVERT: B 74 ASP cc_start: 0.8071 (m-30) cc_final: 0.7654 (m-30) REVERT: B 76 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.4341 (ppt-90) REVERT: B 79 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8108 (mt) REVERT: B 96 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: B 101 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8478 (mptt) REVERT: B 102 ARG cc_start: 0.6770 (mmt180) cc_final: 0.4368 (ttt90) REVERT: B 143 LYS cc_start: 0.8882 (mttm) cc_final: 0.8381 (mttt) REVERT: B 157 ASP cc_start: 0.8151 (t70) cc_final: 0.7840 (t70) REVERT: B 265 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.6323 (m-80) REVERT: B 312 MET cc_start: 0.8545 (ttp) cc_final: 0.7952 (ttp) REVERT: B 316 ARG cc_start: 0.8230 (mtt-85) cc_final: 0.7893 (mtm180) REVERT: C 17 ASP cc_start: 0.8140 (m-30) cc_final: 0.7916 (t70) REVERT: C 101 LYS cc_start: 0.8578 (mmtt) cc_final: 0.7319 (ttpt) REVERT: C 102 ARG cc_start: 0.6456 (mmt180) cc_final: 0.4161 (ptp-170) REVERT: C 181 THR cc_start: 0.8945 (m) cc_final: 0.8434 (p) REVERT: C 294 SER cc_start: 0.8752 (m) cc_final: 0.8454 (t) REVERT: C 311 ARG cc_start: 0.7602 (mtm180) cc_final: 0.7242 (ttm-80) REVERT: C 316 ARG cc_start: 0.7866 (mtt-85) cc_final: 0.5876 (ppt170) REVERT: C 326 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8232 (m110) REVERT: D 17 ASP cc_start: 0.7664 (t0) cc_final: 0.7271 (t0) REVERT: D 18 GLN cc_start: 0.8060 (tt0) cc_final: 0.7717 (mt0) REVERT: D 76 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.4812 (ptt180) REVERT: D 77 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7163 (ppt170) REVERT: D 97 ASP cc_start: 0.7449 (m-30) cc_final: 0.7188 (m-30) REVERT: D 102 ARG cc_start: 0.5792 (mmt180) cc_final: 0.3423 (ptt180) REVERT: D 116 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7552 (mtp-110) REVERT: D 164 LYS cc_start: 0.7900 (tptt) cc_final: 0.7335 (tptt) REVERT: D 183 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7525 (tp30) REVERT: D 235 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7788 (tp30) REVERT: D 302 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7758 (mp) REVERT: D 312 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7612 (tpp) REVERT: E 13 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.5082 (m-80) REVERT: E 52 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8228 (pp20) REVERT: E 102 ARG cc_start: 0.6052 (mmt180) cc_final: 0.3595 (mpp80) REVERT: E 156 TYR cc_start: 0.8569 (m-80) cc_final: 0.8133 (m-80) REVERT: E 159 MET cc_start: 0.8784 (mmt) cc_final: 0.8337 (mmp) REVERT: E 235 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: E 250 TYR cc_start: 0.7998 (m-80) cc_final: 0.7365 (m-80) REVERT: E 311 ARG cc_start: 0.7733 (mtm180) cc_final: 0.7443 (mtm-85) REVERT: E 316 ARG cc_start: 0.7100 (ttm-80) cc_final: 0.5281 (tpt90) REVERT: E 322 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: E 336 MET cc_start: 0.8972 (mmm) cc_final: 0.8588 (mmm) REVERT: F 49 GLN cc_start: 0.8314 (mt0) cc_final: 0.7895 (mt0) REVERT: F 76 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8299 (mtt180) REVERT: F 102 ARG cc_start: 0.6246 (mmt180) cc_final: 0.3638 (pmm-80) REVERT: F 143 LYS cc_start: 0.8962 (mttt) cc_final: 0.8704 (mttp) REVERT: F 157 ASP cc_start: 0.8782 (t70) cc_final: 0.8373 (p0) REVERT: F 159 MET cc_start: 0.8935 (mmm) cc_final: 0.8733 (tpp) REVERT: F 172 ASN cc_start: 0.7677 (p0) cc_final: 0.7430 (p0) REVERT: F 176 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7678 (p0) REVERT: F 196 LEU cc_start: 0.8493 (mt) cc_final: 0.8190 (mp) REVERT: F 224 LYS cc_start: 0.8694 (mtpt) cc_final: 0.7985 (mtpt) REVERT: F 281 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7123 (t0) REVERT: F 312 MET cc_start: 0.8223 (ttt) cc_final: 0.8011 (ttt) REVERT: G 36 VAL cc_start: 0.7964 (p) cc_final: 0.7652 (t) REVERT: G 62 ASP cc_start: 0.7581 (t0) cc_final: 0.7153 (t0) REVERT: H 42 LYS cc_start: 0.8416 (mtpp) cc_final: 0.8065 (mtmt) REVERT: H 79 MET cc_start: 0.8419 (mmt) cc_final: 0.8058 (mmm) REVERT: I 44 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8804 (t) REVERT: I 60 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8788 (tp) REVERT: I 79 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8356 (mpt) outliers start: 165 outliers final: 96 residues processed: 424 average time/residue: 0.6584 time to fit residues: 309.9292 Evaluate side-chains 418 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 294 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 79 MET Chi-restraints excluded: chain I residue 131 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 109 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN D 326 ASN E 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111797 restraints weight = 33512.383| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.82 r_work: 0.3229 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 19746 Z= 0.244 Angle : 0.607 7.057 26754 Z= 0.330 Chirality : 0.047 0.161 2898 Planarity : 0.005 0.058 3534 Dihedral : 8.144 83.493 2782 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Rotamer: Outliers : 8.42 % Allowed : 17.43 % 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: -1.07 (0.16), residues: 2391 helix: 1.39 (0.22), residues: 576 sheet: 0.01 (0.24), residues: 442 loop : -2.01 (0.14), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 125 TYR 0.019 0.002 TYR D 92 PHE 0.032 0.002 PHE D 13 TRP 0.017 0.002 TRP B 155 HIS 0.007 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00579 (19746) covalent geometry : angle 0.60675 (26754) hydrogen bonds : bond 0.06111 ( 702) hydrogen bonds : angle 5.49719 ( 1938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 292 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8514 (p0) REVERT: A 22 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7777 (mp) REVERT: A 47 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8793 (t) REVERT: A 77 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.5092 (ppt-90) REVERT: A 188 MET cc_start: 0.8699 (mmt) cc_final: 0.8335 (mmt) REVERT: A 200 ASP cc_start: 0.7630 (m-30) cc_final: 0.7285 (p0) REVERT: A 219 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7659 (mm) REVERT: A 265 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6520 (m-80) REVERT: A 281 ASP cc_start: 0.6194 (t0) cc_final: 0.5976 (p0) REVERT: A 316 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.6570 (tpt170) REVERT: A 317 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.5615 (ttt180) REVERT: B 74 ASP cc_start: 0.7970 (m-30) cc_final: 0.7553 (m-30) REVERT: B 76 ARG cc_start: 0.6426 (OUTLIER) cc_final: 0.4254 (ppt-90) REVERT: B 77 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.6773 (ppt-90) REVERT: B 96 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: B 101 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8495 (mptt) REVERT: B 102 ARG cc_start: 0.6834 (mmt180) cc_final: 0.4162 (ttt-90) REVERT: B 157 ASP cc_start: 0.8306 (t70) cc_final: 0.8002 (t70) REVERT: B 265 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: B 312 MET cc_start: 0.8526 (ttp) cc_final: 0.7995 (ttp) REVERT: B 316 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7930 (mtm180) REVERT: C 17 ASP cc_start: 0.8146 (m-30) cc_final: 0.7909 (t70) REVERT: C 101 LYS cc_start: 0.8553 (mmtt) cc_final: 0.7305 (ttpt) REVERT: C 102 ARG cc_start: 0.6514 (mmt180) cc_final: 0.4132 (ptp-170) REVERT: C 181 THR cc_start: 0.8995 (m) cc_final: 0.8528 (p) REVERT: C 294 SER cc_start: 0.8745 (m) cc_final: 0.8455 (t) REVERT: C 311 ARG cc_start: 0.7527 (mtm180) cc_final: 0.7179 (ttm-80) REVERT: C 316 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.5855 (ppt170) REVERT: C 326 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8272 (m110) REVERT: D 17 ASP cc_start: 0.7688 (t0) cc_final: 0.7264 (t0) REVERT: D 18 GLN cc_start: 0.8169 (tt0) cc_final: 0.7708 (mt0) REVERT: D 76 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.4717 (ptt180) REVERT: D 77 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7075 (ppt170) REVERT: D 97 ASP cc_start: 0.7467 (m-30) cc_final: 0.7202 (m-30) REVERT: D 102 ARG cc_start: 0.5694 (mmt180) cc_final: 0.3360 (ptt-90) REVERT: D 116 ARG cc_start: 0.7973 (mtp85) cc_final: 0.7744 (mtp-110) REVERT: D 235 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7784 (tp30) REVERT: D 302 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7739 (mp) REVERT: D 312 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7628 (tpp) REVERT: D 336 MET cc_start: 0.8920 (mmm) cc_final: 0.8551 (mmp) REVERT: E 13 PHE cc_start: 0.5187 (OUTLIER) cc_final: 0.4948 (m-80) REVERT: E 102 ARG cc_start: 0.5936 (mmt180) cc_final: 0.3501 (mpp80) REVERT: E 156 TYR cc_start: 0.8551 (m-80) cc_final: 0.8270 (m-80) REVERT: E 159 MET cc_start: 0.8815 (mmt) cc_final: 0.8319 (mmp) REVERT: E 213 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8556 (tp) REVERT: E 235 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: E 316 ARG cc_start: 0.7068 (ttm-80) cc_final: 0.5264 (tpt90) REVERT: E 322 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: E 336 MET cc_start: 0.8978 (mmm) cc_final: 0.8570 (mmm) REVERT: F 49 GLN cc_start: 0.8454 (mt0) cc_final: 0.8051 (mt0) REVERT: F 102 ARG cc_start: 0.6287 (mmt180) cc_final: 0.3690 (pmm-80) REVERT: F 143 LYS cc_start: 0.8953 (mttt) cc_final: 0.8697 (mttp) REVERT: F 157 ASP cc_start: 0.8714 (t70) cc_final: 0.8337 (p0) REVERT: F 172 ASN cc_start: 0.7729 (p0) cc_final: 0.7522 (p0) REVERT: F 224 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8319 (mtmm) REVERT: F 234 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7392 (ttm170) REVERT: F 281 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7119 (t0) REVERT: G 36 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7704 (t) REVERT: G 62 ASP cc_start: 0.7462 (t0) cc_final: 0.6982 (t0) REVERT: H 19 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7092 (tp30) REVERT: H 42 LYS cc_start: 0.8390 (mtpp) cc_final: 0.8052 (mtmt) REVERT: H 60 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7667 (mm) REVERT: H 79 MET cc_start: 0.8369 (mmt) cc_final: 0.8084 (mmm) REVERT: H 113 GLU cc_start: 0.7876 (mp0) cc_final: 0.7625 (mp0) REVERT: I 44 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8829 (t) REVERT: I 60 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8831 (tp) REVERT: I 79 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8397 (mpt) outliers start: 170 outliers final: 107 residues processed: 417 average time/residue: 0.7050 time to fit residues: 327.0573 Evaluate side-chains 410 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 274 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 79 MET Chi-restraints excluded: chain I residue 131 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 91 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 42 optimal weight: 0.0020 chunk 212 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 ASN E 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113156 restraints weight = 33216.100| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.81 r_work: 0.3248 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19746 Z= 0.174 Angle : 0.541 6.199 26754 Z= 0.295 Chirality : 0.045 0.149 2898 Planarity : 0.004 0.055 3534 Dihedral : 7.878 84.579 2780 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 7.92 % Allowed : 18.47 % Favored : 73.60 % 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: -0.93 (0.16), residues: 2391 helix: 1.60 (0.22), residues: 574 sheet: 0.09 (0.24), residues: 437 loop : -1.95 (0.14), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 124 TYR 0.017 0.001 TYR C 92 PHE 0.018 0.002 PHE C 87 TRP 0.016 0.002 TRP B 155 HIS 0.005 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00400 (19746) covalent geometry : angle 0.54116 (26754) hydrogen bonds : bond 0.05303 ( 702) hydrogen bonds : angle 5.33518 ( 1938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 296 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8478 (p0) REVERT: A 22 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.7813 (mp) REVERT: A 47 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8811 (t) REVERT: A 77 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.5065 (ppt-90) REVERT: A 188 MET cc_start: 0.8667 (mmt) cc_final: 0.8402 (mmt) REVERT: A 200 ASP cc_start: 0.7611 (m-30) cc_final: 0.7197 (p0) REVERT: A 219 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7723 (mm) REVERT: A 265 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.6561 (m-80) REVERT: A 281 ASP cc_start: 0.6171 (t0) cc_final: 0.5967 (p0) REVERT: A 316 ARG cc_start: 0.7398 (ttm-80) cc_final: 0.6566 (tpt170) REVERT: A 317 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.5568 (ttt180) REVERT: B 74 ASP cc_start: 0.8027 (m-30) cc_final: 0.7597 (m-30) REVERT: B 76 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.4352 (ppt-90) REVERT: B 77 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.6745 (ppt-90) REVERT: B 96 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: B 101 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8483 (mptt) REVERT: B 102 ARG cc_start: 0.6646 (mmt180) cc_final: 0.4265 (ttt90) REVERT: B 157 ASP cc_start: 0.8131 (t70) cc_final: 0.7827 (t70) REVERT: B 265 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: B 312 MET cc_start: 0.8514 (ttp) cc_final: 0.7963 (ttp) REVERT: B 316 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7905 (mtm180) REVERT: C 17 ASP cc_start: 0.8085 (m-30) cc_final: 0.7831 (t70) REVERT: C 69 HIS cc_start: 0.8156 (m170) cc_final: 0.7739 (m90) REVERT: C 101 LYS cc_start: 0.8539 (mmtt) cc_final: 0.7268 (ttpt) REVERT: C 102 ARG cc_start: 0.6414 (mmt180) cc_final: 0.4086 (ptp-170) REVERT: C 181 THR cc_start: 0.8950 (m) cc_final: 0.8492 (p) REVERT: C 294 SER cc_start: 0.8754 (m) cc_final: 0.8456 (t) REVERT: C 304 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8690 (mtmt) REVERT: C 311 ARG cc_start: 0.7500 (mtm180) cc_final: 0.7193 (ttm-80) REVERT: C 314 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8359 (tm-30) REVERT: C 316 ARG cc_start: 0.7840 (mtt-85) cc_final: 0.5864 (ppt170) REVERT: C 326 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8217 (m110) REVERT: D 17 ASP cc_start: 0.7658 (t0) cc_final: 0.7226 (t0) REVERT: D 18 GLN cc_start: 0.8137 (tt0) cc_final: 0.7710 (mt0) REVERT: D 76 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.4759 (ptt180) REVERT: D 77 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7352 (ppt170) REVERT: D 97 ASP cc_start: 0.7445 (m-30) cc_final: 0.7192 (m-30) REVERT: D 102 ARG cc_start: 0.5652 (mmt180) cc_final: 0.3403 (ptt180) REVERT: D 235 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7825 (tp30) REVERT: D 312 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7601 (tpp) REVERT: D 336 MET cc_start: 0.8917 (mmm) cc_final: 0.8531 (mmp) REVERT: E 13 PHE cc_start: 0.5361 (OUTLIER) cc_final: 0.5037 (m-80) REVERT: E 52 GLU cc_start: 0.8399 (pp20) cc_final: 0.7993 (pp20) REVERT: E 102 ARG cc_start: 0.6008 (mmt180) cc_final: 0.3610 (mpp80) REVERT: E 156 TYR cc_start: 0.8495 (m-80) cc_final: 0.8145 (m-80) REVERT: E 159 MET cc_start: 0.8783 (mmt) cc_final: 0.8300 (mmp) REVERT: E 213 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8557 (tp) REVERT: E 235 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: E 284 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6368 (p0) REVERT: E 316 ARG cc_start: 0.7017 (ttm-80) cc_final: 0.5200 (tpt90) REVERT: E 322 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: E 336 MET cc_start: 0.8981 (mmm) cc_final: 0.8559 (mmm) REVERT: F 49 GLN cc_start: 0.8387 (mt0) cc_final: 0.8038 (mt0) REVERT: F 75 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7699 (mm-40) REVERT: F 102 ARG cc_start: 0.6283 (mmt180) cc_final: 0.3622 (pmm-80) REVERT: F 157 ASP cc_start: 0.8782 (t70) cc_final: 0.8369 (p0) REVERT: F 172 ASN cc_start: 0.7703 (p0) cc_final: 0.7488 (p0) REVERT: F 224 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8281 (mtmm) REVERT: F 281 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7062 (t0) REVERT: G 36 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7687 (t) REVERT: G 62 ASP cc_start: 0.7658 (t0) cc_final: 0.7184 (t0) REVERT: H 19 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: H 42 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8015 (mttt) REVERT: H 79 MET cc_start: 0.8361 (mmt) cc_final: 0.8084 (mmm) REVERT: I 44 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8814 (t) outliers start: 160 outliers final: 101 residues processed: 414 average time/residue: 0.7022 time to fit residues: 322.9555 Evaluate side-chains 406 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 278 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 131 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 3 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 145 optimal weight: 0.0040 chunk 123 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 overall best weight: 6.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 255 HIS D 326 ASN E 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.112350 restraints weight = 33374.071| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.81 r_work: 0.3269 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19746 Z= 0.228 Angle : 0.596 6.821 26754 Z= 0.324 Chirality : 0.047 0.154 2898 Planarity : 0.005 0.058 3534 Dihedral : 8.020 87.627 2777 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 8.42 % Allowed : 18.87 % Favored : 72.71 % 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: -1.09 (0.16), residues: 2391 helix: 1.36 (0.22), residues: 576 sheet: 0.01 (0.24), residues: 437 loop : -2.02 (0.14), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 234 TYR 0.018 0.002 TYR C 92 PHE 0.031 0.002 PHE D 13 TRP 0.016 0.002 TRP B 155 HIS 0.007 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00539 (19746) covalent geometry : angle 0.59603 (26754) hydrogen bonds : bond 0.05913 ( 702) hydrogen bonds : angle 5.45805 ( 1938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 279 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8488 (p0) REVERT: A 22 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.7803 (mp) REVERT: A 47 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8760 (t) REVERT: A 77 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.5075 (ppt-90) REVERT: A 188 MET cc_start: 0.8692 (mmt) cc_final: 0.8333 (mmt) REVERT: A 200 ASP cc_start: 0.7578 (m-30) cc_final: 0.7200 (p0) REVERT: A 219 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7730 (mm) REVERT: A 265 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.6540 (m-80) REVERT: A 281 ASP cc_start: 0.6300 (t0) cc_final: 0.6062 (p0) REVERT: A 316 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.6574 (tpt170) REVERT: A 317 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.5694 (ttp-170) REVERT: B 74 ASP cc_start: 0.8023 (m-30) cc_final: 0.7593 (m-30) REVERT: B 76 ARG cc_start: 0.6541 (OUTLIER) cc_final: 0.4359 (ppt-90) REVERT: B 77 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.6765 (ppt-90) REVERT: B 96 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: B 101 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8496 (mptt) REVERT: B 102 ARG cc_start: 0.6814 (mmt180) cc_final: 0.4208 (ttt-90) REVERT: B 143 LYS cc_start: 0.8939 (mttm) cc_final: 0.8513 (mttt) REVERT: B 157 ASP cc_start: 0.8294 (t70) cc_final: 0.8009 (t70) REVERT: B 265 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.6077 (m-80) REVERT: B 312 MET cc_start: 0.8517 (ttp) cc_final: 0.7996 (ttp) REVERT: B 316 ARG cc_start: 0.8156 (mtt-85) cc_final: 0.7934 (mtm180) REVERT: C 17 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7843 (t70) REVERT: C 79 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8482 (mt) REVERT: C 101 LYS cc_start: 0.8522 (mmtt) cc_final: 0.7336 (ttpt) REVERT: C 102 ARG cc_start: 0.6539 (mmt180) cc_final: 0.4216 (ptp-170) REVERT: C 181 THR cc_start: 0.8971 (m) cc_final: 0.8512 (p) REVERT: C 294 SER cc_start: 0.8757 (m) cc_final: 0.8463 (t) REVERT: C 304 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8610 (mtmt) REVERT: C 311 ARG cc_start: 0.7584 (mtm180) cc_final: 0.7254 (ttm-80) REVERT: C 314 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8337 (tm-30) REVERT: C 316 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.5881 (ppt170) REVERT: C 326 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8267 (m110) REVERT: D 17 ASP cc_start: 0.7716 (t0) cc_final: 0.7301 (t0) REVERT: D 18 GLN cc_start: 0.8002 (tt0) cc_final: 0.7713 (mt0) REVERT: D 76 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.4812 (ptt180) REVERT: D 77 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7050 (ppt170) REVERT: D 97 ASP cc_start: 0.7924 (m-30) cc_final: 0.7646 (m-30) REVERT: D 102 ARG cc_start: 0.5693 (mmt180) cc_final: 0.3425 (ptt-90) REVERT: D 235 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7788 (tp30) REVERT: D 312 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7707 (tpp) REVERT: E 13 PHE cc_start: 0.5273 (OUTLIER) cc_final: 0.5007 (m-80) REVERT: E 102 ARG cc_start: 0.6042 (mmt180) cc_final: 0.3650 (mpp80) REVERT: E 156 TYR cc_start: 0.8524 (m-80) cc_final: 0.8197 (m-80) REVERT: E 159 MET cc_start: 0.8803 (mmt) cc_final: 0.8350 (mmp) REVERT: E 213 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8523 (tp) REVERT: E 235 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: E 284 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6503 (p0) REVERT: E 316 ARG cc_start: 0.6999 (ttm-80) cc_final: 0.5265 (tpt90) REVERT: E 322 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: E 336 MET cc_start: 0.8960 (mmm) cc_final: 0.8559 (mmm) REVERT: F 49 GLN cc_start: 0.8426 (mt0) cc_final: 0.8102 (mt0) REVERT: F 75 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7681 (mm-40) REVERT: F 102 ARG cc_start: 0.6267 (mmt180) cc_final: 0.3762 (pmm-80) REVERT: F 157 ASP cc_start: 0.8629 (t70) cc_final: 0.8308 (p0) REVERT: F 159 MET cc_start: 0.8962 (tpp) cc_final: 0.8717 (mmp) REVERT: F 224 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8241 (mtmm) REVERT: F 281 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7015 (t0) REVERT: G 36 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7730 (t) REVERT: G 62 ASP cc_start: 0.7672 (t0) cc_final: 0.7159 (t0) REVERT: H 19 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7051 (tp30) REVERT: H 42 LYS cc_start: 0.8405 (mtpp) cc_final: 0.8045 (mttt) REVERT: H 79 MET cc_start: 0.8384 (mmt) cc_final: 0.8094 (mmm) REVERT: I 44 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8829 (t) REVERT: I 60 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8825 (tp) outliers start: 170 outliers final: 116 residues processed: 405 average time/residue: 0.6947 time to fit residues: 312.5395 Evaluate side-chains 420 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 274 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 79 MET Chi-restraints excluded: chain I residue 131 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 99 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 ASN D 326 ASN E 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113032 restraints weight = 33267.658| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.80 r_work: 0.3233 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19746 Z= 0.200 Angle : 0.570 6.494 26754 Z= 0.311 Chirality : 0.046 0.150 2898 Planarity : 0.005 0.057 3534 Dihedral : 7.967 89.238 2777 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 8.17 % Allowed : 19.51 % Favored : 72.31 % 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: -1.08 (0.16), residues: 2391 helix: 1.40 (0.22), residues: 576 sheet: -0.03 (0.24), residues: 445 loop : -2.01 (0.14), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 234 TYR 0.018 0.002 TYR C 92 PHE 0.029 0.002 PHE D 13 TRP 0.016 0.002 TRP B 155 HIS 0.006 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00467 (19746) covalent geometry : angle 0.57013 (26754) hydrogen bonds : bond 0.05557 ( 702) hydrogen bonds : angle 5.39311 ( 1938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 282 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8494 (p0) REVERT: A 22 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 47 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8746 (t) REVERT: A 77 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.5066 (ppt-90) REVERT: A 188 MET cc_start: 0.8682 (mmt) cc_final: 0.8332 (mmt) REVERT: A 200 ASP cc_start: 0.7588 (m-30) cc_final: 0.7173 (p0) REVERT: A 219 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7733 (mm) REVERT: A 265 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.6622 (m-80) REVERT: A 281 ASP cc_start: 0.6311 (t0) cc_final: 0.6047 (p0) REVERT: A 316 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.6562 (tpt170) REVERT: A 317 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.5657 (ttp-170) REVERT: B 74 ASP cc_start: 0.7938 (m-30) cc_final: 0.7525 (m-30) REVERT: B 76 ARG cc_start: 0.6508 (OUTLIER) cc_final: 0.4298 (ppt-90) REVERT: B 77 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.6794 (ppt-90) REVERT: B 96 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: B 101 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8373 (mmtm) REVERT: B 102 ARG cc_start: 0.6783 (mmt180) cc_final: 0.4122 (ttt-90) REVERT: B 143 LYS cc_start: 0.8942 (mttm) cc_final: 0.8518 (mttt) REVERT: B 157 ASP cc_start: 0.8325 (t70) cc_final: 0.8033 (t70) REVERT: B 265 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: B 312 MET cc_start: 0.8526 (ttp) cc_final: 0.7981 (ttp) REVERT: B 316 ARG cc_start: 0.8169 (mtt-85) cc_final: 0.7931 (mtm180) REVERT: C 17 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7832 (t70) REVERT: C 69 HIS cc_start: 0.8171 (m170) cc_final: 0.7735 (m90) REVERT: C 101 LYS cc_start: 0.8518 (mmtt) cc_final: 0.7309 (ttpt) REVERT: C 102 ARG cc_start: 0.6431 (mmt180) cc_final: 0.4094 (ptp-170) REVERT: C 181 THR cc_start: 0.8959 (m) cc_final: 0.8498 (p) REVERT: C 294 SER cc_start: 0.8773 (m) cc_final: 0.8463 (t) REVERT: C 304 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8579 (mtmt) REVERT: C 311 ARG cc_start: 0.7548 (mtm180) cc_final: 0.7210 (ttm-80) REVERT: C 314 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8328 (tm-30) REVERT: C 316 ARG cc_start: 0.7832 (mtt-85) cc_final: 0.5852 (ppt170) REVERT: C 326 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8242 (m110) REVERT: D 17 ASP cc_start: 0.7672 (t0) cc_final: 0.7339 (t0) REVERT: D 18 GLN cc_start: 0.8077 (tt0) cc_final: 0.7805 (mt0) REVERT: D 76 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.4772 (ptt180) REVERT: D 77 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7037 (ppt170) REVERT: D 97 ASP cc_start: 0.7879 (m-30) cc_final: 0.7607 (m-30) REVERT: D 102 ARG cc_start: 0.5652 (mmt180) cc_final: 0.3372 (ptt-90) REVERT: D 235 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7785 (tp30) REVERT: D 312 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7647 (tpp) REVERT: E 13 PHE cc_start: 0.5252 (OUTLIER) cc_final: 0.4988 (m-80) REVERT: E 52 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7979 (pp20) REVERT: E 102 ARG cc_start: 0.6054 (mmt180) cc_final: 0.3663 (mpp80) REVERT: E 156 TYR cc_start: 0.8522 (m-80) cc_final: 0.8233 (m-80) REVERT: E 159 MET cc_start: 0.8828 (mmt) cc_final: 0.8372 (mmp) REVERT: E 213 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8565 (tp) REVERT: E 235 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: E 284 ASP cc_start: 0.6696 (OUTLIER) cc_final: 0.6401 (p0) REVERT: E 316 ARG cc_start: 0.7007 (ttm-80) cc_final: 0.5272 (tpt90) REVERT: E 322 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: E 336 MET cc_start: 0.8970 (mmm) cc_final: 0.8553 (mmm) REVERT: F 49 GLN cc_start: 0.8445 (mt0) cc_final: 0.8127 (mt0) REVERT: F 75 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7597 (mm-40) REVERT: F 102 ARG cc_start: 0.6363 (mmt180) cc_final: 0.3739 (pmm-80) REVERT: F 157 ASP cc_start: 0.8644 (t70) cc_final: 0.8297 (p0) REVERT: F 159 MET cc_start: 0.8965 (tpp) cc_final: 0.8716 (mmp) REVERT: F 224 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8258 (mtmm) REVERT: F 281 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7090 (t0) REVERT: G 36 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7692 (t) REVERT: G 62 ASP cc_start: 0.7685 (t0) cc_final: 0.7167 (t0) REVERT: H 19 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7126 (tp30) REVERT: H 42 LYS cc_start: 0.8511 (mtpp) cc_final: 0.8181 (mttt) REVERT: H 79 MET cc_start: 0.8376 (mmt) cc_final: 0.8079 (mmm) REVERT: I 44 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8828 (t) REVERT: I 57 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7569 (tttp) REVERT: I 60 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8804 (tp) REVERT: I 79 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8121 (mpt) outliers start: 165 outliers final: 117 residues processed: 407 average time/residue: 0.7035 time to fit residues: 319.0993 Evaluate side-chains 420 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 271 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 79 MET Chi-restraints excluded: chain I residue 131 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 103 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 ASN D 326 ASN E 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112862 restraints weight = 33241.214| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.80 r_work: 0.3277 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19746 Z= 0.207 Angle : 0.580 7.382 26754 Z= 0.316 Chirality : 0.046 0.151 2898 Planarity : 0.005 0.059 3534 Dihedral : 8.004 89.279 2777 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.06 % Rotamer: Outliers : 8.22 % Allowed : 19.47 % Favored : 72.31 % 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: -1.09 (0.16), residues: 2391 helix: 1.36 (0.22), residues: 576 sheet: 0.01 (0.24), residues: 437 loop : -2.02 (0.14), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 124 TYR 0.018 0.002 TYR C 92 PHE 0.018 0.002 PHE C 87 TRP 0.016 0.002 TRP B 155 HIS 0.006 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00485 (19746) covalent geometry : angle 0.57966 (26754) hydrogen bonds : bond 0.05653 ( 702) hydrogen bonds : angle 5.41219 ( 1938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 277 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8502 (p0) REVERT: A 22 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.7822 (mp) REVERT: A 47 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8747 (t) REVERT: A 77 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.5066 (ppt-90) REVERT: A 188 MET cc_start: 0.8680 (mmt) cc_final: 0.8328 (mmt) REVERT: A 200 ASP cc_start: 0.7610 (m-30) cc_final: 0.7239 (p0) REVERT: A 219 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7755 (mm) REVERT: A 265 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.6530 (m-80) REVERT: A 281 ASP cc_start: 0.6297 (t0) cc_final: 0.6093 (p0) REVERT: A 316 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.6718 (tpt170) REVERT: A 317 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.5703 (ttp-170) REVERT: B 74 ASP cc_start: 0.7954 (m-30) cc_final: 0.7537 (m-30) REVERT: B 76 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.4344 (ppt-90) REVERT: B 77 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.6760 (ppt-90) REVERT: B 96 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: B 101 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8469 (mptt) REVERT: B 102 ARG cc_start: 0.6789 (mmt180) cc_final: 0.4181 (ttt-90) REVERT: B 143 LYS cc_start: 0.8934 (mttm) cc_final: 0.8506 (mttt) REVERT: B 157 ASP cc_start: 0.8137 (t70) cc_final: 0.7846 (t70) REVERT: B 265 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6352 (m-80) REVERT: B 312 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7902 (ttp) REVERT: B 316 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7340 (mtm180) REVERT: C 17 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7829 (t70) REVERT: C 69 HIS cc_start: 0.8172 (m170) cc_final: 0.7739 (m90) REVERT: C 79 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8478 (mt) REVERT: C 101 LYS cc_start: 0.8520 (mmtt) cc_final: 0.7334 (ttpt) REVERT: C 102 ARG cc_start: 0.6459 (mmt180) cc_final: 0.4162 (ptp-170) REVERT: C 181 THR cc_start: 0.8960 (m) cc_final: 0.8515 (p) REVERT: C 294 SER cc_start: 0.8771 (m) cc_final: 0.8469 (t) REVERT: C 304 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8534 (mtmt) REVERT: C 311 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7249 (ttm-80) REVERT: C 314 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8335 (tm-30) REVERT: C 316 ARG cc_start: 0.7849 (mtt-85) cc_final: 0.5883 (ppt170) REVERT: C 326 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8239 (m110) REVERT: D 17 ASP cc_start: 0.7682 (t0) cc_final: 0.7315 (t0) REVERT: D 18 GLN cc_start: 0.8061 (tt0) cc_final: 0.7806 (mt0) REVERT: D 76 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.4812 (ptt180) REVERT: D 77 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7037 (ppt170) REVERT: D 97 ASP cc_start: 0.7891 (m-30) cc_final: 0.7632 (m-30) REVERT: D 102 ARG cc_start: 0.5727 (mmt180) cc_final: 0.3524 (ptt-90) REVERT: D 235 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7786 (tp30) REVERT: D 312 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7642 (tpp) REVERT: E 13 PHE cc_start: 0.5259 (OUTLIER) cc_final: 0.5009 (m-80) REVERT: E 52 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7908 (pp20) REVERT: E 102 ARG cc_start: 0.5992 (mmt180) cc_final: 0.3671 (mpp80) REVERT: E 156 TYR cc_start: 0.8541 (m-80) cc_final: 0.8271 (m-80) REVERT: E 159 MET cc_start: 0.8853 (mmt) cc_final: 0.8439 (mmp) REVERT: E 213 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8514 (tp) REVERT: E 235 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: E 284 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6402 (p0) REVERT: E 316 ARG cc_start: 0.7045 (ttm-80) cc_final: 0.5327 (tpt90) REVERT: E 322 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: E 336 MET cc_start: 0.8964 (mmm) cc_final: 0.8573 (mmm) REVERT: F 49 GLN cc_start: 0.8435 (mt0) cc_final: 0.8119 (mt0) REVERT: F 102 ARG cc_start: 0.6372 (mmt180) cc_final: 0.3802 (pmm-80) REVERT: F 157 ASP cc_start: 0.8627 (t70) cc_final: 0.8308 (p0) REVERT: F 159 MET cc_start: 0.8953 (tpp) cc_final: 0.8705 (mmp) REVERT: F 224 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8241 (mtmm) REVERT: F 281 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7078 (t0) REVERT: G 36 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7718 (t) REVERT: G 62 ASP cc_start: 0.7682 (t0) cc_final: 0.7163 (t0) REVERT: H 19 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7121 (tp30) REVERT: H 42 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8169 (mtmt) REVERT: H 79 MET cc_start: 0.8377 (mmt) cc_final: 0.8084 (mmm) REVERT: I 44 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8826 (t) REVERT: I 60 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8822 (tp) REVERT: I 79 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8190 (mpt) outliers start: 166 outliers final: 118 residues processed: 401 average time/residue: 0.7113 time to fit residues: 317.3863 Evaluate side-chains 413 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 263 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 79 MET Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 135 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 173 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 ASN D 326 ASN E 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113086 restraints weight = 33194.057| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.80 r_work: 0.3279 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19746 Z= 0.196 Angle : 0.569 7.399 26754 Z= 0.310 Chirality : 0.045 0.150 2898 Planarity : 0.005 0.059 3534 Dihedral : 7.963 88.374 2777 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 7.78 % Allowed : 20.16 % Favored : 72.07 % 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: -1.08 (0.16), residues: 2391 helix: 1.39 (0.22), residues: 576 sheet: -0.01 (0.24), residues: 445 loop : -2.02 (0.14), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 124 TYR 0.018 0.002 TYR C 92 PHE 0.035 0.002 PHE D 13 TRP 0.016 0.002 TRP B 155 HIS 0.006 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00455 (19746) covalent geometry : angle 0.56944 (26754) hydrogen bonds : bond 0.05510 ( 702) hydrogen bonds : angle 5.37384 ( 1938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 277 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8497 (p0) REVERT: A 22 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.7817 (mp) REVERT: A 47 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8760 (t) REVERT: A 77 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.5040 (ppt-90) REVERT: A 188 MET cc_start: 0.8674 (mmt) cc_final: 0.8327 (mmt) REVERT: A 200 ASP cc_start: 0.7596 (m-30) cc_final: 0.7239 (p0) REVERT: A 219 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7744 (mm) REVERT: A 265 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.6569 (m-80) REVERT: A 281 ASP cc_start: 0.6286 (t0) cc_final: 0.6067 (p0) REVERT: A 316 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.6572 (tpt170) REVERT: A 317 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.5703 (ttp-170) REVERT: B 74 ASP cc_start: 0.7964 (m-30) cc_final: 0.7546 (m-30) REVERT: B 76 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.4359 (ppt-90) REVERT: B 77 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.6771 (ppt-90) REVERT: B 96 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: B 101 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8382 (mmtm) REVERT: B 102 ARG cc_start: 0.6777 (mmt180) cc_final: 0.4181 (ttt90) REVERT: B 143 LYS cc_start: 0.8932 (mttm) cc_final: 0.8506 (mttt) REVERT: B 157 ASP cc_start: 0.8140 (t70) cc_final: 0.7852 (t70) REVERT: B 265 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6568 (m-80) REVERT: B 312 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7970 (ttp) REVERT: B 316 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7356 (mtm180) REVERT: C 17 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7814 (t70) REVERT: C 69 HIS cc_start: 0.8149 (m170) cc_final: 0.7728 (m90) REVERT: C 79 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8501 (mt) REVERT: C 101 LYS cc_start: 0.8513 (mmtt) cc_final: 0.7327 (ttpt) REVERT: C 102 ARG cc_start: 0.6454 (mmt180) cc_final: 0.4164 (ptp-170) REVERT: C 181 THR cc_start: 0.8944 (m) cc_final: 0.8505 (p) REVERT: C 294 SER cc_start: 0.8768 (m) cc_final: 0.8462 (t) REVERT: C 304 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8531 (mtmt) REVERT: C 311 ARG cc_start: 0.7498 (mtm180) cc_final: 0.7124 (ttm-80) REVERT: C 314 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8312 (tm-30) REVERT: C 316 ARG cc_start: 0.7840 (mtt-85) cc_final: 0.5883 (ppt170) REVERT: C 326 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8232 (m110) REVERT: D 17 ASP cc_start: 0.7630 (t0) cc_final: 0.7259 (t0) REVERT: D 76 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.4810 (ptt180) REVERT: D 77 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7025 (ppt170) REVERT: D 97 ASP cc_start: 0.7878 (m-30) cc_final: 0.7621 (m-30) REVERT: D 102 ARG cc_start: 0.5732 (mmt180) cc_final: 0.3541 (ptt-90) REVERT: D 235 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7769 (tp30) REVERT: D 312 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7668 (tpp) REVERT: E 12 GLN cc_start: 0.3948 (pm20) cc_final: 0.2752 (pm20) REVERT: E 13 PHE cc_start: 0.5245 (OUTLIER) cc_final: 0.4976 (m-80) REVERT: E 52 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7958 (pp20) REVERT: E 102 ARG cc_start: 0.6062 (mmt180) cc_final: 0.3718 (mpp80) REVERT: E 156 TYR cc_start: 0.8534 (m-80) cc_final: 0.8273 (m-80) REVERT: E 159 MET cc_start: 0.8849 (mmt) cc_final: 0.8443 (mmp) REVERT: E 213 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8554 (tp) REVERT: E 235 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: E 284 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.6391 (p0) REVERT: E 316 ARG cc_start: 0.7039 (ttm-80) cc_final: 0.5323 (tpt90) REVERT: E 322 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: E 336 MET cc_start: 0.8964 (mmm) cc_final: 0.8573 (mmm) REVERT: F 49 GLN cc_start: 0.8421 (mt0) cc_final: 0.8113 (mt0) REVERT: F 102 ARG cc_start: 0.6359 (mmt180) cc_final: 0.3819 (pmm-80) REVERT: F 157 ASP cc_start: 0.8623 (t70) cc_final: 0.8306 (p0) REVERT: F 159 MET cc_start: 0.8947 (tpp) cc_final: 0.8702 (mmp) REVERT: F 224 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8156 (mtmm) REVERT: F 281 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7067 (t0) REVERT: G 36 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7735 (t) REVERT: G 62 ASP cc_start: 0.7668 (t0) cc_final: 0.7168 (t0) REVERT: H 19 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: H 42 LYS cc_start: 0.8501 (mtpp) cc_final: 0.8159 (mtmt) REVERT: H 79 MET cc_start: 0.8378 (mmt) cc_final: 0.8089 (mmm) REVERT: I 44 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8829 (t) REVERT: I 57 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7495 (tttp) REVERT: I 79 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8181 (mpt) outliers start: 157 outliers final: 117 residues processed: 399 average time/residue: 0.7034 time to fit residues: 312.2387 Evaluate side-chains 419 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 270 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 79 MET Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 135 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 79 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 168 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 ASN D 326 ASN E 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114522 restraints weight = 33099.272| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.81 r_work: 0.3275 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19746 Z= 0.148 Angle : 0.528 7.018 26754 Z= 0.287 Chirality : 0.044 0.149 2898 Planarity : 0.004 0.061 3534 Dihedral : 7.711 88.455 2777 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 7.03 % Allowed : 21.10 % Favored : 71.87 % 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: -0.91 (0.16), residues: 2391 helix: 1.59 (0.22), residues: 574 sheet: 0.07 (0.24), residues: 450 loop : -1.93 (0.14), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 311 TYR 0.017 0.001 TYR C 92 PHE 0.034 0.001 PHE D 13 TRP 0.018 0.002 TRP B 155 HIS 0.005 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00331 (19746) covalent geometry : angle 0.52812 (26754) hydrogen bonds : bond 0.04825 ( 702) hydrogen bonds : angle 5.22367 ( 1938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 281 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8470 (p0) REVERT: A 22 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.7817 (mp) REVERT: A 47 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8817 (t) REVERT: A 77 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.5051 (ppt-90) REVERT: A 124 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8159 (ptp90) REVERT: A 188 MET cc_start: 0.8657 (mmt) cc_final: 0.8404 (mmt) REVERT: A 200 ASP cc_start: 0.7563 (m-30) cc_final: 0.7167 (p0) REVERT: A 219 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7718 (mm) REVERT: A 265 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: A 281 ASP cc_start: 0.6283 (t0) cc_final: 0.6061 (p0) REVERT: A 316 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.6569 (tpt170) REVERT: A 317 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.5665 (ttp-170) REVERT: B 74 ASP cc_start: 0.8055 (m-30) cc_final: 0.7621 (m-30) REVERT: B 76 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.4355 (ppt-90) REVERT: B 77 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.6757 (ppt-90) REVERT: B 96 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: B 101 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8458 (mptt) REVERT: B 102 ARG cc_start: 0.6568 (mmt180) cc_final: 0.4299 (ttt90) REVERT: B 143 LYS cc_start: 0.8947 (mttm) cc_final: 0.8519 (mttt) REVERT: B 157 ASP cc_start: 0.8155 (t70) cc_final: 0.7872 (t70) REVERT: B 192 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8396 (m) REVERT: B 265 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.6632 (m-80) REVERT: B 312 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8000 (ttp) REVERT: B 316 ARG cc_start: 0.8121 (mtt-85) cc_final: 0.7336 (mtm180) REVERT: C 17 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7800 (t70) REVERT: C 69 HIS cc_start: 0.8038 (m170) cc_final: 0.7569 (m90) REVERT: C 101 LYS cc_start: 0.8535 (mmtt) cc_final: 0.7268 (ttpt) REVERT: C 102 ARG cc_start: 0.6424 (mmt180) cc_final: 0.4142 (ptp-170) REVERT: C 181 THR cc_start: 0.8905 (m) cc_final: 0.8446 (p) REVERT: C 294 SER cc_start: 0.8774 (m) cc_final: 0.8465 (t) REVERT: C 304 LYS cc_start: 0.8864 (mttt) cc_final: 0.8519 (mtmt) REVERT: C 311 ARG cc_start: 0.7449 (mtm180) cc_final: 0.7078 (ttm-80) REVERT: C 314 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8356 (tm-30) REVERT: C 316 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.5853 (ppt170) REVERT: C 326 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8213 (m110) REVERT: D 17 ASP cc_start: 0.7628 (t0) cc_final: 0.7215 (t0) REVERT: D 20 GLU cc_start: 0.7920 (mp0) cc_final: 0.7589 (mp0) REVERT: D 76 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.4793 (ptt180) REVERT: D 77 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7322 (ppt170) REVERT: D 97 ASP cc_start: 0.7842 (m-30) cc_final: 0.7615 (m-30) REVERT: D 102 ARG cc_start: 0.6078 (mmt180) cc_final: 0.3771 (ptt180) REVERT: D 192 SER cc_start: 0.8794 (p) cc_final: 0.8363 (t) REVERT: D 312 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7606 (tpp) REVERT: E 13 PHE cc_start: 0.5275 (OUTLIER) cc_final: 0.5011 (m-80) REVERT: E 52 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7946 (pp20) REVERT: E 102 ARG cc_start: 0.5941 (mmt180) cc_final: 0.3657 (mpp80) REVERT: E 156 TYR cc_start: 0.8512 (m-80) cc_final: 0.8168 (m-80) REVERT: E 159 MET cc_start: 0.8788 (mmt) cc_final: 0.8357 (mmp) REVERT: E 284 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6178 (t0) REVERT: E 316 ARG cc_start: 0.6984 (ttm-80) cc_final: 0.5369 (tpt90) REVERT: E 322 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: F 49 GLN cc_start: 0.8418 (mt0) cc_final: 0.8091 (mt0) REVERT: F 102 ARG cc_start: 0.6183 (mmt180) cc_final: 0.3652 (pmm-80) REVERT: F 121 GLU cc_start: 0.8823 (tp30) cc_final: 0.8536 (tp30) REVERT: F 157 ASP cc_start: 0.8620 (t70) cc_final: 0.8299 (p0) REVERT: F 159 MET cc_start: 0.8990 (tpp) cc_final: 0.8760 (mmp) REVERT: F 224 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8175 (mtmm) REVERT: G 36 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7659 (t) REVERT: H 42 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8115 (mtmt) REVERT: H 79 MET cc_start: 0.8380 (mmt) cc_final: 0.8092 (mmm) REVERT: I 50 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8272 (p) REVERT: I 57 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7481 (tttp) REVERT: I 79 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8071 (mpt) outliers start: 142 outliers final: 100 residues processed: 389 average time/residue: 0.6936 time to fit residues: 299.7833 Evaluate side-chains 394 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 267 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 243 ASP Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 79 MET Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 135 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 30 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 ASN E 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.125088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114213 restraints weight = 33206.505| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.81 r_work: 0.3295 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19746 Z= 0.161 Angle : 0.543 7.713 26754 Z= 0.295 Chirality : 0.044 0.149 2898 Planarity : 0.004 0.061 3534 Dihedral : 7.652 87.846 2773 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.02 % Favored : 95.94 % Rotamer: Outliers : 6.64 % Allowed : 21.59 % Favored : 71.77 % 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: -0.88 (0.16), residues: 2391 helix: 1.61 (0.22), residues: 573 sheet: 0.19 (0.24), residues: 442 loop : -1.93 (0.14), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 311 TYR 0.016 0.001 TYR C 92 PHE 0.017 0.001 PHE C 87 TRP 0.017 0.002 TRP D 155 HIS 0.005 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00364 (19746) covalent geometry : angle 0.54344 (26754) hydrogen bonds : bond 0.05001 ( 702) hydrogen bonds : angle 5.23683 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7762.07 seconds wall clock time: 132 minutes 26.03 seconds (7946.03 seconds total)